GenomeSmasher FAQ
Q. I am trying to run the SV_generator.sh but I’m only getting Novel insertions – no Large deletions, CNVs, inversions or translocations.
A. This script expects at least 19 different chromosome.fa files in the Genome_DIR. If you are only wanting to simulate variants on one or a few chromosomes, just copy the part of the script you want.
perl $SCRIPTS_DIR/Large_Deletions.pl $CHROMOSOME $OUTPUT_VCF 20
Q. When running SNP_mutator_v2.pl, how do I know how many variants to simulate?
A. You can choose whatever you want. If one assumes the genome has 3M variants on 23 chromosomes, then you should simulate ~130k per chromosome. Alternatively, you can just randomly subset variants from the dbSNP vcf file. Just make sure to remove multi-allelic variants (i.e. those with a comma in the alt field).
Page last modified: October 24, 2014