### get the gene chromosome and position for BRCA1:
bior@biordev:/data/catalogs/NCBIGene/GRCh37_p10$ zcat genes.tsv.bgz | grep -P '^17\t' | grep "BRCA1"
17	41196312	41277500	{"_type":"gene","_landmark":"17","_strand":"-","_minBP":41196312,"_maxBP":41277500,"gene":"BRCA1","gene_synonym":"BRCAI; BRCC1; BROVCA1; IRIS; PNCA4; PPP1R53; PSCP; RNF53","note":"breast cancer 1, early onset; Derived by automated computational analysis using gene prediction method: BestRefseq.","GeneID":"672","HGNC":"1100","HPRD":"00218","MIM":"113705"}

### Perform a tabix search on BGI to get the total # of variants within that range:
bior@biordev:/data/catalogs/BGI/hg19$ tabix LuCAMP_200exomeFinal_hg19.tsv.bgz 17:41196312-41277500 | wc
     22      88   11767
bior@biordev:/data/catalogs/BGI/hg19$ tabix LuCAMP_200exomeFinal_hg19.tsv.bgz 17:41196312-41277500
17	41197708	41197708	{"chromosome_id":"chr17","genomic_position":38451234,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":2,"minor_allele":"G","number_A":2,"number_C":1,"number_G":127,"number_T":1253,"estimated_minor_allele_freq":0.091387,"estimated_major_allele_freq":0.908613,"calculated_minor_allele_freq":0.0918293564714389,"calculated_major_allele_freq":0.9060014461315979,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"T","_altAlleles":["G"],"_minBP":41197708,"_maxBP":41197708,"_type":"variant","_id":"."}
17	41215825	41215825	{"chromosome_id":"chr17","genomic_position":38469351,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":1,"number_C":1399,"number_G":2,"number_T":567,"estimated_minor_allele_freq":0.287959,"estimated_major_allele_freq":0.7120409999999999,"calculated_minor_allele_freq":0.28796343321482987,"calculated_major_allele_freq":0.7105129507364144,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41215825,"_maxBP":41215825,"_type":"variant","_id":"."}
17	41219560	41219560	{"chromosome_id":"chr17","genomic_position":38473086,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":3,"number_C":1919,"number_G":2,"number_T":656,"estimated_minor_allele_freq":0.241025,"estimated_major_allele_freq":0.758975,"calculated_minor_allele_freq":0.25426356589147286,"calculated_major_allele_freq":0.743798449612403,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41219560,"_maxBP":41219560,"_type":"variant","_id":"."}
***17	41219596	41219596	{"chromosome_id":"chr17","genomic_position":38473122,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":2574,"number_C":2,"number_G":14,"number_T":1,"estimated_minor_allele_freq":8.5E-4,"estimated_major_allele_freq":0.99915,"calculated_minor_allele_freq":0.005403319181783096,"calculated_major_allele_freq":0.9934388267078348,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41219596,"_maxBP":41219596,"_type":"variant","_id":"."}
17	41222975	41222975	{"chromosome_id":"chr17","genomic_position":38476501,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":2,"number_C":4278,"number_G":0,"number_T":61,"estimated_minor_allele_freq":0.008867,"estimated_major_allele_freq":0.991133,"calculated_minor_allele_freq":0.014052061736926975,"calculated_major_allele_freq":0.9854872149274361,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41222975,"_maxBP":41222975,"_type":"variant","_id":"."}
***17	41223094	41223094	{"chromosome_id":"chr17","genomic_position":38476620,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":6,"number_C":1099,"number_G":1,"number_T":2818,"estimated_minor_allele_freq":0.280026,"estimated_major_allele_freq":0.719974,"calculated_minor_allele_freq":0.28007135575942915,"calculated_major_allele_freq":0.718144750254842,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41223094,"_maxBP":41223094,"_type":"variant","_id":"."}
17	41234470	41234470	{"chromosome_id":"chr17","genomic_position":38487996,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":4160,"number_C":2,"number_G":1557,"number_T":4,"estimated_minor_allele_freq":0.275641,"estimated_major_allele_freq":0.724359,"calculated_minor_allele_freq":0.27206010833478944,"calculated_major_allele_freq":0.7268914904770225,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41234470,"_maxBP":41234470,"_type":"variant","_id":"."}
17	41243509	41243509	{"chromosome_id":"chr17","genomic_position":38497035,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":0,"number_C":26,"number_G":0,"number_T":2361,"estimated_minor_allele_freq":0.009117,"estimated_major_allele_freq":0.990883,"calculated_minor_allele_freq":0.010892333472978634,"calculated_major_allele_freq":0.9891076665270213,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41243509,"_maxBP":41243509,"_type":"variant","_id":"."}
17	41243891	41243891	{"chromosome_id":"chr17","genomic_position":38497417,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":2,"minor_allele":"G","number_A":4,"number_C":3626,"number_G":12,"number_T":0,"estimated_minor_allele_freq":0.0,"estimated_major_allele_freq":1.0,"calculated_minor_allele_freq":0.0032948929159802307,"calculated_major_allele_freq":0.9956068094453597,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"C","_altAlleles":["G"],"_minBP":41243891,"_maxBP":41243891,"_type":"variant","_id":"."}
17	41244000	41244000	{"chromosome_id":"chr17","genomic_position":38497526,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":2,"number_C":1113,"number_G":1,"number_T":2726,"estimated_minor_allele_freq":0.286308,"estimated_major_allele_freq":0.713692,"calculated_minor_allele_freq":0.2896928682977616,"calculated_major_allele_freq":0.7095262883914628,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244000,"_maxBP":41244000,"_type":"variant","_id":"."}
17	41244130	41244130	{"chromosome_id":"chr17","genomic_position":38497656,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":1,"number_C":12,"number_G":1,"number_T":3154,"estimated_minor_allele_freq":1.24E-4,"estimated_major_allele_freq":0.999876,"calculated_minor_allele_freq":0.003787878787878788,"calculated_major_allele_freq":0.9955808080808081,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244130,"_maxBP":41244130,"_type":"variant","_id":"."}
17	41244132	41244132	{"chromosome_id":"chr17","genomic_position":38497658,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":0,"minor_allele":"A","number_A":9,"number_C":3120,"number_G":1,"number_T":5,"estimated_minor_allele_freq":0.0,"estimated_major_allele_freq":1.0,"calculated_minor_allele_freq":0.0028708133971291866,"calculated_major_allele_freq":0.9952153110047847,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"C","_altAlleles":["A"],"_minBP":41244132,"_maxBP":41244132,"_type":"variant","_id":"."}
17	41244246	41244246	{"chromosome_id":"chr17","genomic_position":38497772,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":7,"number_C":4195,"number_G":5,"number_T":21,"estimated_minor_allele_freq":0.0,"estimated_major_allele_freq":1.0,"calculated_minor_allele_freq":0.004966887417218543,"calculated_major_allele_freq":0.9921948912015137,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41244246,"_maxBP":41244246,"_type":"variant","_id":"."}
17	41244429	41244429	{"chromosome_id":"chr17","genomic_position":38497955,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":3,"number_C":3259,"number_G":3,"number_T":102,"estimated_minor_allele_freq":0.025935,"estimated_major_allele_freq":0.974065,"calculated_minor_allele_freq":0.030294030294030293,"calculated_major_allele_freq":0.967923967923968,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41244429,"_maxBP":41244429,"_type":"variant","_id":"."}
17	41244435	41244435	{"chromosome_id":"chr17","genomic_position":38497961,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":1,"number_C":826,"number_G":3,"number_T":2480,"estimated_minor_allele_freq":0.265384,"estimated_major_allele_freq":0.7346159999999999,"calculated_minor_allele_freq":0.24954682779456194,"calculated_major_allele_freq":0.7492447129909365,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244435,"_maxBP":41244435,"_type":"variant","_id":"."}
***17	41244936	41244936	{"chromosome_id":"chr17","genomic_position":38498462,"index_of_major_allele":2,"major_allele":"G","index_of_minor_allele":0,"minor_allele":"A","number_A":1122,"number_C":1,"number_G":2973,"number_T":4,"estimated_minor_allele_freq":0.290568,"estimated_major_allele_freq":0.7094320000000001,"calculated_minor_allele_freq":0.2736585365853659,"calculated_major_allele_freq":0.7251219512195122,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41244936,"_maxBP":41244936,"_type":"variant","_id":"."}
17	41245237	41245237	{"chromosome_id":"chr17","genomic_position":38498763,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":3096,"number_C":1,"number_G":1093,"number_T":0,"estimated_minor_allele_freq":0.280233,"estimated_major_allele_freq":0.719767,"calculated_minor_allele_freq":0.26085918854415274,"calculated_major_allele_freq":0.7389021479713603,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41245237,"_maxBP":41245237,"_type":"variant","_id":"."}
17	41245466	41245466	{"chromosome_id":"chr17","genomic_position":38498992,"index_of_major_allele":2,"major_allele":"G","index_of_minor_allele":0,"minor_allele":"A","number_A":1031,"number_C":2,"number_G":3019,"number_T":43,"estimated_minor_allele_freq":0.276816,"estimated_major_allele_freq":0.723184,"calculated_minor_allele_freq":0.25177045177045176,"calculated_major_allele_freq":0.7372405372405373,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41245466,"_maxBP":41245466,"_type":"variant","_id":"."}
17	41245471	41245471	{"chromosome_id":"chr17","genomic_position":38498997,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":2,"number_C":4140,"number_G":12,"number_T":247,"estimated_minor_allele_freq":0.052664,"estimated_major_allele_freq":0.947336,"calculated_minor_allele_freq":0.05612360827084754,"calculated_major_allele_freq":0.9406952965235174,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41245471,"_maxBP":41245471,"_type":"variant","_id":"."}
17	41246481	41246481	{"chromosome_id":"chr17","genomic_position":38500007,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":2,"number_C":313,"number_G":0,"number_T":3448,"estimated_minor_allele_freq":0.079046,"estimated_major_allele_freq":0.920954,"calculated_minor_allele_freq":0.08317831517406325,"calculated_major_allele_freq":0.9162901939941536,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41246481,"_maxBP":41246481,"_type":"variant","_id":"."}
17	41256101	41256101	{"chromosome_id":"chr17","genomic_position":38509627,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":760,"number_C":1,"number_G":144,"number_T":2,"estimated_minor_allele_freq":0.192087,"estimated_major_allele_freq":0.807913,"calculated_minor_allele_freq":0.1587651598676957,"calculated_major_allele_freq":0.8379272326350606,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41256101,"_maxBP":41256101,"_type":"variant","_id":"."}
17	41256103	41256103	{"chromosome_id":"chr17","genomic_position":38509629,"index_of_major_allele":2,"major_allele":"G","index_of_minor_allele":0,"minor_allele":"A","number_A":204,"number_C":0,"number_G":737,"number_T":0,"estimated_minor_allele_freq":0.232495,"estimated_major_allele_freq":0.767505,"calculated_minor_allele_freq":0.21679064824654623,"calculated_major_allele_freq":0.7832093517534537,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41256103,"_maxBP":41256103,"_type":"variant","_id":"."}

### Num of variants in dbSNP that fall within the BRCA1 range
bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | wc
   2780   11120 1270426

### Num of variants in dbSNP that are the same variant within BGI that fall within the BRCA1 range
bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | bior_same_variant -d /data/catalogs/BGI/hg19/LuCAMP_200exomeFinal_hg19.tsv.bgz | grep -v "{}" | wc
     20     100   20028

bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | bior_same_variant -d /data/catalogs/BGI/hg19/LuCAMP_200exomeFinal_hg19.tsv.bgz | grep -v "{}"
#UNKNOWN_1	UNKNOWN_2	UNKNOWN_3	UNKNOWN_4	SameVariantPipe
17	41197708	41197708	{"CHROM":"17","POS":"41197708","ID":"rs201196020","REF":"T","ALT":"G","QUAL":".","FILTER":".","INFO":{"RSPOS":41197708,"dbSNPBuildID":137,"SSR":0,"SAO":0,"VP":"050000800a05070002000100","WGT":1,"VC":"SNV","NSM":true,"REF":true,"U3":true,"ASP":true,"VLD":true,"G5A":true,"G5":true,"OTHERKG":true},"_id":"rs201196020","_type":"variant","_landmark":"17","_refAllele":"T","_altAlleles":["G"],"_minBP":41197708,"_maxBP":41197708}	{"chromosome_id":"chr17","genomic_position":38451234,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":2,"minor_allele":"G","number_A":2,"number_C":1,"number_G":127,"number_T":1253,"estimated_minor_allele_freq":0.091387,"estimated_major_allele_freq":0.908613,"calculated_minor_allele_freq":0.0918293564714389,"calculated_major_allele_freq":0.9060014461315979,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"T","_altAlleles":["G"],"_minBP":41197708,"_maxBP":41197708,"_type":"variant","_id":"."}
17	41215825	41215825	{"CHROM":"17","POS":"41215825","ID":"rs3092994","REF":"C","ALT":"T","QUAL":".","FILTER":".","INFO":{"RSPOS":41215825,"RV":true,"GMAF":0.3127,"dbSNPBuildID":103,"SSR":0,"SAO":0,"VP":"05016808000507051f100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"INT":true,"ASP":true,"VLD":true,"G5A":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPilot123":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs3092994","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41215825,"_maxBP":41215825}	{"chromosome_id":"chr17","genomic_position":38469351,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":1,"number_C":1399,"number_G":2,"number_T":567,"estimated_minor_allele_freq":0.287959,"estimated_major_allele_freq":0.7120409999999999,"calculated_minor_allele_freq":0.28796343321482987,"calculated_major_allele_freq":0.7105129507364144,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41215825,"_maxBP":41215825,"_type":"variant","_id":"."}
17	41219560	41219560	{"CHROM":"17","POS":"41219560","ID":"rs8176235","REF":"C","ALT":"T","QUAL":".","FILTER":".","INFO":{"RSPOS":41219560,"RV":true,"GMAF":0.2692,"dbSNPBuildID":117,"SSR":0,"SAO":0,"VP":"050100080005070517000100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","SLO":true,"INT":true,"ASP":true,"VLD":true,"G5A":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPROD":true,"OTHERKG":true,"PH3":true},"_id":"rs8176235","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41219560,"_maxBP":41219560}	{"chromosome_id":"chr17","genomic_position":38473086,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":3,"number_C":1919,"number_G":2,"number_T":656,"estimated_minor_allele_freq":0.241025,"estimated_major_allele_freq":0.758975,"calculated_minor_allele_freq":0.25426356589147286,"calculated_major_allele_freq":0.743798449612403,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41219560,"_maxBP":41219560,"_type":"variant","_id":"."}
17	41222975	41222975	{"CHROM":"17","POS":"41222975","ID":"rs1799967","REF":"C","ALT":"T","QUAL":".","FILTER":".","INFO":{"RSPOS":41222975,"RV":true,"GMAF":0.0092,"dbSNPBuildID":89,"SSR":0,"SAO":0,"VP":"050360000a05040517100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"S3D":true,"SLO":true,"NSM":true,"REF":true,"ASP":true,"VLD":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs1799967","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41222975,"_maxBP":41222975}	{"chromosome_id":"chr17","genomic_position":38476501,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":2,"number_C":4278,"number_G":0,"number_T":61,"estimated_minor_allele_freq":0.008867,"estimated_major_allele_freq":0.991133,"calculated_minor_allele_freq":0.014052061736926975,"calculated_major_allele_freq":0.9854872149274361,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41222975,"_maxBP":41222975,"_type":"variant","_id":"."}
17	41234470	41234470	{"CHROM":"17","POS":"41234470","ID":"rs1060915","REF":"A","ALT":"G","QUAL":".","FILTER":".","INFO":{"RSPOS":41234470,"RV":true,"GMAF":0.3036,"dbSNPBuildID":86,"SSR":0,"SAO":0,"VP":"05016800030505051f100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"REF":true,"SYN":true,"ASP":true,"VLD":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPilot123":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs1060915","_type":"variant","_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41234470,"_maxBP":41234470}	{"chromosome_id":"chr17","genomic_position":38487996,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":4160,"number_C":2,"number_G":1557,"number_T":4,"estimated_minor_allele_freq":0.275641,"estimated_major_allele_freq":0.724359,"calculated_minor_allele_freq":0.27206010833478944,"calculated_major_allele_freq":0.7268914904770225,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41234470,"_maxBP":41234470,"_type":"variant","_id":"."}
17	41243509	41243509	{"CHROM":"17","POS":"41243509","ID":"rs28897689","REF":"T","ALT":"C","QUAL":".","FILTER":".","INFO":{"RSPOS":41243509,"RV":true,"GMAF":9.0E-4,"dbSNPBuildID":125,"SSR":0,"SAO":0,"VP":"050160080805040517100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"VLD":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs28897689","_type":"variant","_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41243509,"_maxBP":41243509}	{"chromosome_id":"chr17","genomic_position":38497035,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":0,"number_C":26,"number_G":0,"number_T":2361,"estimated_minor_allele_freq":0.009117,"estimated_major_allele_freq":0.990883,"calculated_minor_allele_freq":0.010892333472978634,"calculated_major_allele_freq":0.9891076665270213,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41243509,"_maxBP":41243509,"_type":"variant","_id":"."}
17	41243891	41243891	{"CHROM":"17","POS":"41243891","ID":"rs80356876","REF":"C","ALT":"G","QUAL":".","FILTER":".","INFO":{"RSPOS":41243891,"RV":true,"dbSNPBuildID":132,"SSR":0,"SAO":0,"VP":"050160080801000002100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"SLO":true,"NSM":true,"INT":true,"OTHERKG":true,"LSD":true},"_id":"rs80356876","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["G"],"_minBP":41243891,"_maxBP":41243891}	{"chromosome_id":"chr17","genomic_position":38497417,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":2,"minor_allele":"G","number_A":4,"number_C":3626,"number_G":12,"number_T":0,"estimated_minor_allele_freq":0.0,"estimated_major_allele_freq":1.0,"calculated_minor_allele_freq":0.0032948929159802307,"calculated_major_allele_freq":0.9956068094453597,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"C","_altAlleles":["G"],"_minBP":41243891,"_maxBP":41243891,"_type":"variant","_id":"."}
17	41244000	41244000	{"CHROM":"17","POS":"41244000","ID":"rs16942","REF":"T","ALT":"C","QUAL":".","FILTER":".","INFO":{"RSPOS":41244000,"RV":true,"GMAF":0.3242,"dbSNPBuildID":60,"SSR":0,"SAO":0,"VP":"05016808080507051f100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"VLD":true,"G5A":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPilot123":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs16942","_type":"variant","_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244000,"_maxBP":41244000}	{"chromosome_id":"chr17","genomic_position":38497526,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":2,"number_C":1113,"number_G":1,"number_T":2726,"estimated_minor_allele_freq":0.286308,"estimated_major_allele_freq":0.713692,"calculated_minor_allele_freq":0.2896928682977616,"calculated_major_allele_freq":0.7095262883914628,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244000,"_maxBP":41244000,"_type":"variant","_id":"."}
17	41244130	41244130	{"CHROM":"17","POS":"41244130","ID":"rs2227945","REF":"T","ALT":"C","QUAL":".","FILTER":".","INFO":{"RSPOS":41244130,"RV":true,"GMAF":0.0114,"dbSNPBuildID":98,"SSR":0,"SAO":0,"VP":"050160080805050517100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"VLD":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs2227945","_type":"variant","_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244130,"_maxBP":41244130}	{"chromosome_id":"chr17","genomic_position":38497656,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":1,"number_C":12,"number_G":1,"number_T":3154,"estimated_minor_allele_freq":1.24E-4,"estimated_major_allele_freq":0.999876,"calculated_minor_allele_freq":0.003787878787878788,"calculated_major_allele_freq":0.9955808080808081,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244130,"_maxBP":41244130,"_type":"variant","_id":"."}
17	41244132	41244132	{"CHROM":"17","POS":"41244132","ID":"rs80357228","REF":"C","ALT":"A","QUAL":".","FILTER":".","INFO":{"RSPOS":41244132,"RV":true,"dbSNPBuildID":132,"SSR":0,"SAO":0,"VP":"050160080801000002100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"SLO":true,"NSM":true,"INT":true,"OTHERKG":true,"LSD":true},"_id":"rs80357228","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["A"],"_minBP":41244132,"_maxBP":41244132}	{"chromosome_id":"chr17","genomic_position":38497658,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":0,"minor_allele":"A","number_A":9,"number_C":3120,"number_G":1,"number_T":5,"estimated_minor_allele_freq":0.0,"estimated_major_allele_freq":1.0,"calculated_minor_allele_freq":0.0028708133971291866,"calculated_major_allele_freq":0.9952153110047847,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"C","_altAlleles":["A"],"_minBP":41244132,"_maxBP":41244132,"_type":"variant","_id":"."}
17	41244246	41244246	{"CHROM":"17","POS":"41244246","ID":"rs41293447","REF":"C","ALT":"T","QUAL":".","FILTER":".","INFO":{"RSPOS":41244246,"RV":true,"dbSNPBuildID":127,"SSR":0,"SAO":0,"VP":"050160080805000002100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"OTHERKG":true,"LSD":true},"_id":"rs41293447","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41244246,"_maxBP":41244246}	{"chromosome_id":"chr17","genomic_position":38497772,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":7,"number_C":4195,"number_G":5,"number_T":21,"estimated_minor_allele_freq":0.0,"estimated_major_allele_freq":1.0,"calculated_minor_allele_freq":0.004966887417218543,"calculated_major_allele_freq":0.9921948912015137,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41244246,"_maxBP":41244246,"_type":"variant","_id":"."}
17	41244429	41244429	{"CHROM":"17","POS":"41244429","ID":"rs4986852","REF":"C","ALT":"T","QUAL":".","FILTER":".","INFO":{"RSPOS":41244429,"RV":true,"GMAF":0.0119,"dbSNPBuildID":113,"SSR":0,"SAO":1,"VP":"050168080805050517110101","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"VLD":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true,"OM":true,"GCF":true},"_id":"rs4986852","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41244429,"_maxBP":41244429{"chromosome_id":"chr17","genomic_position":38497955,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":3,"number_C":3259,"number_G":3,"number_T":102,"estimated_minor_allele_freq":0.025935,"estimated_major_allele_freq":0.974065,"calculated_minor_allele_freq":0.030294030294030293,"calculated_major_allele_freq":0.967923967923968,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41244429,"_maxBP":41244429,"_type":"variant","_id":"."}
17	41244435	41244435	{"CHROM":"17","POS":"41244435","ID":"rs16941","REF":"T","ALT":"C","QUAL":".","FILTER":".","INFO":{"RSPOS":41244435,"RV":true,"GMAF":0.3031,"dbSNPBuildID":60,"SSR":0,"SAO":0,"VP":"05016808080505051f100101","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"VLD":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPilot123":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true,"GCF":true},"_id":"rs16941","_type":"variant","_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244435,"_maxBP":41244435}	{"chromosome_id":"chr17","genomic_position":38497961,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":1,"number_C":826,"number_G":3,"number_T":2480,"estimated_minor_allele_freq":0.265384,"estimated_major_allele_freq":0.7346159999999999,"calculated_minor_allele_freq":0.24954682779456194,"calculated_major_allele_freq":0.7492447129909365,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41244435,"_maxBP":41244435,"_type":"variant","_id":"."}
17	41245237	41245237	{"CHROM":"17","POS":"41245237","ID":"rs16940","REF":"A","ALT":"G","QUAL":".","FILTER":".","INFO":{"RSPOS":41245237,"RV":true,"GMAF":0.3017,"dbSNPBuildID":60,"SSR":0,"SAO":0,"VP":"05016808010507051f100101","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"SYN":true,"INT":true,"ASP":true,"VLD":true,"G5A":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPilot123":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true,"GCF":true},"_id":"rs16940","_type":"variant","_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41245237,"_maxBP":41245237}	{"chromosome_id":"chr17","genomic_position":38498763,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":3096,"number_C":1,"number_G":1093,"number_T":0,"estimated_minor_allele_freq":0.280233,"estimated_major_allele_freq":0.719767,"calculated_minor_allele_freq":0.26085918854415274,"calculated_major_allele_freq":0.7389021479713603,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41245237,"_maxBP":41245237,"_type":"variant","_id":"."}
17	41245466	41245466	{"CHROM":"17","POS":"41245466","ID":"rs1799949","REF":"G","ALT":"A","QUAL":".","FILTER":".","INFO":{"RSPOS":41245466,"RV":true,"GMAF":0.3242,"dbSNPBuildID":89,"SSR":0,"SAO":0,"VP":"05016808010505051f100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"SYN":true,"INT":true,"ASP":true,"VLD":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPilot123":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs1799949","_type":"variant","_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41245466,"_maxBP":41245466}	{"chromosome_id":"chr17","genomic_position":38498992,"index_of_major_allele":2,"major_allele":"G","index_of_minor_allele":0,"minor_allele":"A","number_A":1031,"number_C":2,"number_G":3019,"number_T":43,"estimated_minor_allele_freq":0.276816,"estimated_major_allele_freq":0.723184,"calculated_minor_allele_freq":0.25177045177045176,"calculated_major_allele_freq":0.7372405372405373,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41245466,"_maxBP":41245466,"_type":"variant","_id":"."}
17	41245471	41245471	{"CHROM":"17","POS":"41245471","ID":"rs4986850","REF":"C","ALT":"T","QUAL":".","FILTER":".","INFO":{"RSPOS":41245471,"RV":true,"GMAF":0.0398,"dbSNPBuildID":113,"SSR":0,"SAO":0,"VP":"050168080805050517100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"VLD":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs4986850","_type":"variant","_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41245471,"_maxBP":41245471}	{"chromosome_id":"chr17","genomic_position":38498997,"index_of_major_allele":1,"major_allele":"C","index_of_minor_allele":3,"minor_allele":"T","number_A":2,"number_C":4140,"number_G":12,"number_T":247,"estimated_minor_allele_freq":0.052664,"estimated_major_allele_freq":0.947336,"calculated_minor_allele_freq":0.05612360827084754,"calculated_major_allele_freq":0.9406952965235174,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"C","_altAlleles":["T"],"_minBP":41245471,"_maxBP":41245471,"_type":"variant","_id":"."}
17	41246481	41246481	{"CHROM":"17","POS":"41246481","ID":"rs1799950","REF":"T","ALT":"C","QUAL":".","FILTER":".","INFO":{"RSPOS":41246481,"RV":true,"GMAF":0.0279,"dbSNPBuildID":89,"SSR":0,"SAO":0,"VP":"050168080805050517100100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","PM":true,"PMC":true,"SLO":true,"NSM":true,"INT":true,"ASP":true,"VLD":true,"G5":true,"HD":true,"GNO":true,"KGPhase1":true,"KGPROD":true,"OTHERKG":true,"PH3":true,"LSD":true},"_id":"rs1799950","_type":"variant","_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41246481,"_maxBP":41246481}	{"chromosome_id":"chr17","genomic_position":38500007,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":2,"number_C":313,"number_G":0,"number_T":3448,"estimated_minor_allele_freq":0.079046,"estimated_major_allele_freq":0.920954,"calculated_minor_allele_freq":0.08317831517406325,"calculated_major_allele_freq":0.9162901939941536,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41246481,"_maxBP":41246481,"_type":"variant","_id":"."}
17	41256101	41256101	{"CHROM":"17","POS":"41256101","ID":"rs45456891","REF":"A","ALT":"G","QUAL":".","FILTER":".","INFO":{"RSPOS":41256101,"RV":true,"dbSNPBuildID":127,"SSR":0,"SAO":0,"VP":"050000080015000002000100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","INT":true,"OTH":true,"ASP":true,"OTHERKG":true},"_id":"rs45456891","_type":"variant","_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41256101,"_maxBP":41256101}	{"chromosome_id":"chr17","genomic_position":38509627,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":760,"number_C":1,"number_G":144,"number_T":2,"estimated_minor_allele_freq":0.192087,"estimated_major_allele_freq":0.807913,"calculated_minor_allele_freq":0.1587651598676957,"calculated_major_allele_freq":0.8379272326350606,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41256101,"_maxBP":41256101,"_type":"variant","_id":"."}
17	41256103	41256103	{"CHROM":"17","POS":"41256103","ID":"rs45569832","REF":"G","ALT":"A","QUAL":".","FILTER":".","INFO":{"RSPOS":41256103,"RV":true,"dbSNPBuildID":127,"SSR":16,"SAO":0,"VP":"050000080005000002000100","GENEINFO":"BRCA1:672","WGT":1,"VC":"SNV","INT":true,"ASP":true,"OTHERKG":true},"_id":"rs45569832","_type":"variant","_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41256103,"_maxBP":41256103}	{"chromosome_id":"chr17","genomic_position":38509629,"index_of_major_allele":2,"major_allele":"G","index_of_minor_allele":0,"minor_allele":"A","number_A":204,"number_C":0,"number_G":737,"number_T":0,"estimated_minor_allele_freq":0.232495,"estimated_major_allele_freq":0.767505,"calculated_minor_allele_freq":0.21679064824654623,"calculated_major_allele_freq":0.7832093517534537,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41256103,"_maxBP":41256103,"_type":"variant","_id":"."}

### Drill out the minBP in each json (from dbSNP and BGI) and append to end so we can compare side-to-side:
### NOTE: The json columns are lost when drilling
bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | bior_same_variant -d /data/catalogs/BGI/hg19/LuCAMP_200exomeFinal_hg19.tsv.bgz | grep -v "{}" | bior_drill --column 4 --path "_minBP" | bior_drill  --column 4 --path "_minBP"
#UNKNOWN_1	UNKNOWN_2	UNKNOWN_3	_minBP	_minBP
17	41197708	41197708	41197708	41197708
17	41215825	41215825	41215825	41215825
17	41219560	41219560	41219560	41219560
17	41222975	41222975	41222975	41222975
17	41234470	41234470	41234470	41234470
17	41243509	41243509	41243509	41243509
17	41243891	41243891	41243891	41243891
17	41244000	41244000	41244000	41244000
17	41244130	41244130	41244130	41244130
17	41244132	41244132	41244132	41244132
17	41244246	41244246	41244246	41244246
17	41244429	41244429	41244429	41244429
17	41244435	41244435	41244435	41244435
17	41245237	41245237	41245237	41245237
17	41245466	41245466	41245466	41245466
17	41245471	41245471	41245471	41245471
17	41246481	41246481	41246481	41246481
17	41256101	41256101	41256101	41256101
17	41256103	41256103	41256103	41256103

### So what about the 3 that were in BGI but not found in dbSNP?
***17	41219596	41219596	{"chromosome_id":"chr17","genomic_position":38473122,"index_of_major_allele":0,"major_allele":"A","index_of_minor_allele":2,"minor_allele":"G","number_A":2574,"number_C":2,"number_G":14,"number_T":1,"estimated_minor_allele_freq":8.5E-4,"estimated_major_allele_freq":0.99915,"calculated_minor_allele_freq":0.005403319181783096,"calculated_major_allele_freq":0.9934388267078348,"is_in_dbSNP":0,"_landmark":"17","_refAllele":"A","_altAlleles":["G"],"_minBP":41219596,"_maxBP":41219596,"_type":"variant","_id":"."}
***17	41223094	41223094	{"chromosome_id":"chr17","genomic_position":38476620,"index_of_major_allele":3,"major_allele":"T","index_of_minor_allele":1,"minor_allele":"C","number_A":6,"number_C":1099,"number_G":1,"number_T":2818,"estimated_minor_allele_freq":0.280026,"estimated_major_allele_freq":0.719974,"calculated_minor_allele_freq":0.28007135575942915,"calculated_major_allele_freq":0.718144750254842,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"T","_altAlleles":["C"],"_minBP":41223094,"_maxBP":41223094,"_type":"variant","_id":"."}
***17	41244936	41244936	{"chromosome_id":"chr17","genomic_position":38498462,"index_of_major_allele":2,"major_allele":"G","index_of_minor_allele":0,"minor_allele":"A","number_A":1122,"number_C":1,"number_G":2973,"number_T":4,"estimated_minor_allele_freq":0.290568,"estimated_major_allele_freq":0.7094320000000001,"calculated_minor_allele_freq":0.2736585365853659,"calculated_major_allele_freq":0.7251219512195122,"is_in_dbSNP":1,"_landmark":"17","_refAllele":"G","_altAlleles":["A"],"_minBP":41244936,"_maxBP":41244936,"_type":"variant","_id":"."}

### Let's try overlap (instead of sameVariant) to see if we get all the same variants:
bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | bior_overlap -d /data/catalogs/BGI/hg19/LuCAMP_200exomeFinal_hg19.tsv.bgz | grep -v "{}" | wc
     33     165   32848
### WHY IS IT COMING BACK WITH 33 (31 UNIQUES WHEN THERE ARE ONLY 22 VARIANTS IN THE REGION FOR BGI!!!!!!!???????????)
bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | bior_overlap -d /data/catalogs/BGI/hg19/LuCAMP_200exomeFinal_hg19.tsv.bgz | grep -v "{}"
#UNKNOWN_1	UNKNOWN_2	UNKNOWN_3	UNKNOWN_4	OverlapPipe
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### EUREKA!!!!!  It is because of the multiple base-pair Variants (where ref is > 1 base-pair), which causes several to overlap each other
### So, everything appears to be ok.
bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | grep -P '\"REF\":\"[A|C|G|T]' | bior_same_variant -d /data/catalogs/BGI/hg19/LuCAMP_200exomeFinal_hg19.tsv.bgz  | grep -v "{}" | wc
     20     100   20028
bior@biordev:/data/catalogs/dbSNP/137$ tabix 00-All_GRCh37.tsv.bgz 17:41196312-41277500 | grep -P '\"REF\":\"[A|C|G|T]' | bior_same_variant -d /data/catalogs/BGI/hg19/LuCAMP_200exomeFinal_hg19.tsv.bgz  | grep -v "{}" 
#UNKNOWN_1	UNKNOWN_2	UNKNOWN_3	UNKNOWN_4	SameVariantPipe
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