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Question: How to extract entire info column from VCF file using bcftools
0
gravatar for Tails
22 months ago by
Tails • 60
New Zealand
Tails • 60 wrote:

I want to extract the whole info column, and the documentation indicates that %INFO should extract the whole info column.

https://samtools.github.io/bcftools/bcftools.html#query

I've tried the following:

bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t%INFO[\t%SAMPLE=%AD]\n' file.vcf

But I get an error saying it cannot parse format string.

The reason I want the whole info column is that there are about 20 different fields there and I don't want to extract them one by one.
snp bcftools software error • 1.9k views
ADD COMMENT • link •
modified 22 months ago by finswimmer ♦ 14k • written 22 months ago by Tails • 60
0
gravatar for finswimmer
22 months ago by
finswimmer ♦ 14k
Germany
finswimmer ♦ 14k wrote:

Hello,

unfortunately this is not possible. See here: https://github.com/samtools/bcftools/issues/637

If you have a good reason why you need it and cut isn't enough, please leave a comment in this issue. Maybe it will be implemented.

fin swimmer

ADD COMMENT • link written 22 months ago by finswimmer ♦ 14k

Indeed, and, with cut or awk, you can still merge these via paste to output of bcftools query, which is still very useful to use to extract tag information that is embedded in INFO or FORMAT:

paste \
  <(bcftools view test.bcf | \
    awk '!/^#/ {print $1":"$2":"$4":"$5}') \
  <(bcftools query --samples 2610,2661,6313,6318 -f '%CHROM\t%POS\t%REF\t%ALT\t%DP\t[%AD\t]\n' test.bcf) \
  | head -10
1:65797:T:C 1   65797   T   C   5012    .   .   .   .   
1:65841:T:G 1   65841   T   G   3234    .   .   .   .   
1:65851:C:T 1   65851   C   T   3271    .   .   .   .   
1:65872:T:G 1   65872   T   G   32370   236,39  .   .   205,47  
1:65918:C:T 1   65918   C   T   8629    .   .   .   232,0   
1:65974:A:G 1   65974   A   G   7623    .   .   .   .   
1:65999:G:C 1   65999   G   C   1767    .   .   .   .   
1:66162:A:T 1   66162   A   T   805 1,1 3,1 .   1,2 
1:69270:A:G 1   69270   A   G   1064    .   .   .   .   
1:69428:T:G 1   69428   T   G   870 .   .   .   .
ADD REPLY • link written 22 months ago by Kevin Blighe ♦ 71k
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