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SelectVariants - Exclude variants shared with a certain genotype

WestcottWestcott BerkeleyMember

Hi all,

I'm using a non-model organism to call variants on some UV generated mutants. The reference genome is not perfect, so I sequenced WT along side my mutants. I'm now to my final, filtered .vcf file and I'd like to use SelectVariants to filter out any variants that are shared among the mutants and WT.

So far, I've tried the -xl_se flag followed by my sample names:

-T SelectVariants -R ref.fasta -V All_Variants.vcf -o WT_excluded_variants.vcf -xl_se 'WT.CzWTSNP' -xl_se 'WT.CzWTINDL'

This returns a .vcf with WT removed, but the mutant variants shared among WT remain.

I'm pretty sure that this is a simple task, but I can't seem to figure it out. Any suggestions would be welcome.


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