Read position bias (RPB and PV4) fields from samtools mpileup: how to get them?
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3.4 years ago
Macspider ★ 3.4k

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?

mpileup variant SNP call RPB • 1.2k views
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2
Entering edit mode
3.4 years ago
al.bodrug ▴ 50

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

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2.4 years ago
al.bodrug ▴ 50

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

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