Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?

Question

[Matteo Schiavinato]

Hi all,

How does anyone get the RPB and the PV4 into their VCF file? I can't ask for them in mpileup -t <tags> and I can't ask for them anywhere else (or so I think).

Here are the supported samtools mpileup tags at the moment: http://www.htslib.org/doc/samtools-1.0.html#mpileup

Can someone help me?

Answer 1

[al.bodrug]

Here it the latest version of samtools manual: http://www.htslib.org/doc/samtools.html PV4 field disappears.

Answer 2

[al.bodrug]

Note: PV4 seems to be supported /appear only when you call the variants with -c parameter in bcftools