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 ) & isRef( GEN ) | isHet( GEN ) && \
isHom( GEN ) & isRef( GEN ) | isHet( GEN ) && \
isHom( GEN ) & isRef( GEN ) | isHet( GEN ) && \"