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samtools v1.3: AD, ADF and ADR fields.

In the new version of samtools, additional fields to INFO column can be added such as AD, ADF and ADR:

  • AD: Total allelic depth
  • ADF: Total allelic depths on the forward strand
  • ADR: Total allelic depths on the reverse strand

According to the manual, each of the mentioned tags have the following format (for ADR for example): Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases. Everything is OK.

My question is: Why sometimes (for some variants), I'm getting only 3 of the 4 counters? Ex.:

> chr1  52  .   C   G   19.4215 .   DP=5;VDB=0.1;SGB=-0.453602;RPB=0;MQB=0.75;BQB=1;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=2,0,2,0;MQ=45    GT:PL:DP:ADF:ADR:AD:GQ  0/1:52,0,67:4:2,2,0:0,0,0:2,2,0:54
> chr1  141 .   T   A   164 .   DP=32;VDB=2.5082e-05;SGB=-0.670168;RPB=0.958048;MQB=0.92664;MQSB=0.960728;BQB=0.79189;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=6,1,7,3;MQ=44  GT:PL:DP:ADF:ADR:AD:GQ  0/1:197,0,151:17:6,7,0,0:1,1,2,0:7,8,2,0:127

Here you can see it in clearer:

GT:PL:DP:ADF:ADR:AD:GQ

0/1:52,0,67:4:2,2,0:0,0,0:2,2,0:54

0/1:197,0,151:17:6,7,0,0:1,1,2,0:7,8,2,0:127

EDIT: For some variants I'm seeing also only 2 counters. Any clue?

EDIT_2: Reading a little bit more... I've found this definition: AD=Allelic depths for the ref and alt alleles in the order listed. So, I interpret that there are as many AD values as there are alleles, but... as can be observed in the above example, in both cases I've only 2 alleles (one REF and one ALT).

samtools sam format
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written by iraun iraun

How did you obtain your data? Did you use something like vcf_parser file.vcf --split?

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written by kulvait kulvait

This sound like a good question, anybody have an answer to that ?

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written by Rob Rob

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