Question: samtools v1.3: AD, ADF and ADR fields.
gravatar for iraun
4.2 years ago by
iraun3.7k wrote:

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:




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).

sam samtools format • 3.7k views
ADD COMMENTlink modified 3.7 years ago • written 4.2 years ago by iraun3.7k

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

ADD REPLYlink written 4.1 years ago by kulvait250

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

ADD REPLYlink written 3.8 years ago by Rob120
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 655 users visited in the last hour