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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