Question: bcftools split and filter variants in vcf
2
cmccabe • 180 wrote:
I use bcftools norm to split and left-normalize variants (like the line in file). After norm the variant is split correctly and annotated, my question is can the AF tag be used to filter out AF= below 20% in the command or is there another? So in this case the first split vatiant is filtered out. Thank you :).
before bcftools norm
chr4 187004216 . TC T,TT
after bcftools norm
chr4 187004217 187004217 C -
AF=0.0305344;AO=130
chr4 187004217 187004217 C T
AF=0.969466;AO=673
desired output
chr4 187004217 187004217 C T
AF=0.969466;AO=673
ADD COMMENT
• link
•
modified 12 months ago
by
Kevin Blighe ♦ 37k
•
written
12 months ago by
cmccabe • 180
