The manpage for bcftools annotate -c suggests trying something like:
bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%FORMAT/DPR\t%FORMAT/DP4\n'
results.vcf | head
Don't know where else in the manpage this appears.
- tom blackwell -
On Wed, 29 Oct 2014, jbr950 wrote:
> Hello,
> I'd like to avoid writing my own parser, using stock 'bcftools query'
> for its intended purpose instead.
>
> I need to extract the DP4 field, and the command I'm issuing is not
> including it:
>
> First I check that DP4 is actually present in my vcf:
>
> grep "<X" results.vcf | head -2
> 1 10397540 . T <X> 0 .
> DP=15;I16=11,4,0,0,535,19161,0,0,300,6000,0,0,238,4626,0,0;QS=1,0;MQSB=1;MQ0F=0;DPR=15,0
> PL:DP4:DPR 0,45,146:11,4,0,0:15,0
> 1 10397541 . G <X> 0 .
> DP=15;I16=11,4,0,0,514,17700,0,0,300,6000,0,0,235,4541,0,0;QS=1,0;MQSB=1;MQ0F=0;DPR=15,0
> PL:DP4:DPR 0,45,146:11,4,0,0:15,0
>
>
>
> Then I try bcftools query:
> $bcftools_htslib_path/bcftools query
> -f'%CHROM\t%POS\t%REF\t%ALT\t%DPR\t%DP4\n' results.vcf | head
> 1 10397540 T <X> 15,0 .
> 1 10397541 G <X> 15,0 .
> 1 10397542 C <X> 15,0 .
> 1 10397543 A <X> 15,0 .
> 1 10397544 G <X> 15,0 .
> 1 10397545 G <X> 15,0 .
> 1 10397546 C <X> 15,0 .
> 1 10397547 C <X> 16,0 .
> 1 10397548 A <X> 17,0 .
> 1 10397549 G <X> 17,0 .
>
>
> Is there a way to adjust my command, or is this a bug?
>
> Best,
> Jonathan
>
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