HI Tom,
Good find! Unfortunately, that didn't help, bcftools query doesn't
seem to recognize the suggested syntax of FORMAT/DP4, if I've constructed
the request in the appropriate manner.
$bcftools_htslib_path/bcftools query
-f'%CHROM\t%POS\t%REF\t%ALT\t%DPR\t%FORMAT/DP4\n' results.vcf | head
Error: no such tag defined in the VCF header: INFO/FORMAT
The original call:
$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 .
Thanks for the suggestion,
Jonathan
On Wed, Oct 29, 2014 at 3:28 PM, Thomas W. Blackwell <tbla...@umich.edu>
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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