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

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

• 2,498 views • link

updated 7.2 years ago by al.bodrug

• written 8.2 years ago by Matteo Schiavinato

2 answers

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

• 1 views • link

written 8.2 years ago by al.bodrug

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

• 0 views • link

written 7.2 years ago by al.bodrug

More posts like this

VCF file, calculate depth per sample
written 4.5 years ago by pixie@bioinfo

Hello, I have GBS data with a fairly large raw vcf file. I wanted to generate some quick custom stats. I wanted to find the …
Samtools pileup extract read length for position
written 5.1 years ago by rah •

I am working with bam files and vcf files, where i wish to extract the read length for those reads which overlaps with the positions …
missing informations in VCF file (read mapping)
written 5.5 years ago by romain.derelle •

HI, I've mapped paired end Illumina reads on a genome and generated, using samtools and bcftools a VCF file containing all SNPs. My commands were, …
Pipe pysam.view() output to pysam.sort()
written 6.8 years ago by Matteo Schiavinato

Hi everyone, I am trying to pipe `pysam.view()` into `pysam.sort()` in a program. Since both are wrappers for **samtools**, it is quite easy to read …
How can I add PV4 or BQ or NS to my VCF file
written 8.7 years ago by sahar.voghoei •

I am trying to extract maximum features for my machine learning input, and I need PV4, BQ, G3, NS to be added to my VCF …
Samtools mpileup: AF1 and DP4 not provided
written 8.7 years ago by filippo.martignano •

Hello! I'm using this command line: samtools mpileup SAMPLE.bam -f GENOME.fasta -B -d 1000 -R -Q 20 -l BEDFILE.bed -t ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -v > OUTPUT.vcf and …
suggested value for SP (Phred-scaled strand bias P-value) Samtools mpileup
written 8.8 years ago by filippo.martignano •

Hi everyone! i'm setting up the --output-tags in my samtools mpileup command line. I want also to include SP (Phred-scaled strand bias P-value), according to …
GiaB SV Calls for NIST:HG001/NA12878: What's the reference build?
written 9.4 years ago by QVINTVS_FABIVS_MAXIMVS

You would think NIST/GiaB would explicitly state the reference build for their putative gold standard SV calls. But I can't see it anywhere I'm assuming …
samtools vcf output disagree with mpileup in DP
written 10.4 years ago by DVA

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 …
Add Dp Tag To Genotype Field Of Vcf File
written 13.1 years ago by jetsejacobi •

<p>Hello everyone,</p> <p>I am using <a href='http://samtools.sourceforge.net/'>samtools</a> mpileup for SNP calling, then with BEAGLE I do the haplotyping and with GATK BeagleOutputToVCF I convert the …