I tried to understand the output of
bcftools mpileup, especially the
In this case,
I16=0,9878,0,28,..., the total reads are
9878+28=9906, that not equal to the
According to the description in header of
vcf file for
I16 tag, the first four numbers are:
// depth fwd .. ref (0) and non-ref (2) // depth rev .. ref (1) and non-ref (3)
The sum of the four number supposed (I think!?) to equal to
DP (raw read depth) number, but it is not.
So, I have two questions:
- Is there any default filtering that will change the first four numbers in
I16? what is it?
- How can I tell the exact the depth for each of the
ALTbases? (C, G, A in this case).
The following are the command and one line of the results:
$ bcftools mpileup -d 10000 -f ref.fa align.bam > mpileup.vcf $ grep -P "\t311\t" mpileup.vcf ref 311 . T C,G,A 0 . DP=9953;I16=0,9878,0,28,397088,1.60422e+07,588,12502,592680,3.55608e+07,1680,100800,19953,41405,56,112;QS=0.998521,0.00121707,0.00019111,7.04091e-05;VDB=1.30483e-15;SGB=-0.693054;RPB=0.998703;MQB=1;BQB=1.00562e-18;MQ0F=0 PL 0,255,255,255,255,255,255,255,255,255 ## bcftools v1.9