Hi Shane,
That did the trick; thanks!
$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 11,4,0,0
1 10397541 G <X> 15,0 11,4,0,0
1 10397542 C <X> 15,0 11,4,0,0
1 10397543 A <X> 15,0 11,4,0,0
1 10397544 G <X> 15,0 11,4,0,0
1 10397545 G <X> 15,0 11,4,0,0
1 10397546 C <X> 15,0 11,4,0,0
1 10397547 C <X> 16,0 11,5,0,0
1 10397548 A <X> 17,0 12,5,0,0
1 10397549 G <X> 17,0 12,5,0,0
Best,
Jonathan
On Wed, Oct 29, 2014 at 3:49 PM, Shane McCarthy <s...@sanger.ac.uk> wrote:
> To loop over FORMAT fields, you need the square brackets, so:
>
> bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%DPR\t%DP4]\n' results.vcf
>
> Shane
>
>
> On 29 Oct 2014, at 19:28, Thomas W. Blackwell wrote:
>
> >
> > 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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