BCftools call when using -v -V indels vs using -V indels only
please can you explain to me why this happened to me ? when using bcftools flags -v (variants only) and -V indels i get only 50% of the snps in the sample even so if i only use -V indels and subsequent QC with plink it retains 98% of the called snps why is that?
in simple words -v when combine with -V indels does something not right for my data ..if -v really filters real variants , plink would have done it. is that coz i used the -i flag for mpileup ?
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