Hello,

I'm having a hard time understand the "DP" tag for .VCF output from samtools mpileup. The number seems much smaller than the read depth in .pileup output for a same position. Here are my codes:

To generate .pileup file:

samtools mpileup -q 1 -f $REF $SAMPLE.sort.rudup.test.bam > $SAMPLE.pileup

The output looks like (there is more "." than what is shown here) below, with coverage = 8000, which is the max depth set by samtools, and means there is possibly more than 8000:

 chrM    68      G       8000    ..................................................................................................................................................................................................................................................................C..........................................................................................

To generate .vcf file:

samtools mpileup -uf $REF -q 1 $SAMPLE.sort.rudup.test.bam -v -t DP,DV,DPR,DP4,SP > $SAMPLE.vc.test.vcf

The output looks like below, with DP=615, which is much less than 8000:

chrM    68  .   G   C,<X>   0   .   DP=615;I16=613,0,2,0,24095,974979,22,242,27695,1.47356e+06,62,3604,14930,367588,41,881;QS=0.999268,0.000731886,0;VDB=0.56;SGB=-0.453602;RPB=0.875204;MQB=0.76509;BQB=0.0375204;MQ0F=0   PL:DP:DV:SP:DP4:DPR 0,255,255,255,255,255:615:2:0:613,0,2,0:613,2,0

I also tried to remove the filter for base quality (-Q 0) when generating VCF, but it does not change the output DP - it only seems to change the first value of I16. Does anyone know what do I miss here please? (Also, I don't quite get the <x> in the ALT column and would appreciate some explanation for it).

Thank you very much.