SNPsift
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8 weeks ago

I have a vcf file with samples from one species called against the reference genome of an other species. I am trying to remove sites any sites fixed among my samples for non reference alleles.

I have constructed this code below for the 11 samples in my vcf file. I am not sure if this is the correct logic for what I am attempting to filter from my vcf file (I included an example for just three samples for simplicity of the post!). I have not been able to find any direction on other posts and would very much appreciate any suggestions or guidance. Thank you!!

zcat D.al.snps.11samples.0.75missing.biallelic.vcf.gz |\
SnpSift filter \


"isHom( GEN[0] ) & isRef( GEN[0] ) | isHet( GEN[0] ) && \ isHom( GEN[1] ) & isRef( GEN[1] ) | isHet( GEN[1] ) && \ isHom( GEN[2] ) & isRef( GEN[2] ) | isHet( GEN[2] ) && \"

alleles filter SNPsift nonrefence • 125 views