Question: bcftools split and filter variants in vcf
2
gravatar for cmccabe
12 months ago by
cmccabe180
Chicago
cmccabe180 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
bcftools ngs • 742 views
ADD COMMENTlink modified 12 months ago by Kevin Blighe37k • written 12 months ago by cmccabe180
2
gravatar for Kevin Blighe
12 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

You are certainly correct to normalise the file prior to filtering; otherwise, you would obtain unexpected results.

To filter on AF, use bcftools view, specifically the following parameters:

-q/Q, --min-af/--max-af

Kevin

ADD COMMENTlink written 12 months ago by Kevin Blighe37k
1

Thank you very much :).

ADD REPLYlink written 12 months ago by cmccabe180
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