davidyuyuan

Updating filter syntax and threshold ?

1

I could be very wrong. The syntax and threshold values in the example might be outdated in Filtering variants on https://samtools.github.io/bcftools/howtos/variant-calling.html: ``` bcftools filter -sLowQual -g3 -G10 \ -e'%QUAL

(I was unable to find an answer by reading the documentation.) If an input VCF is partially phased, would Shapeit5 apply its phasing logic to all variants regardless they are...