VCF to gVCF conversion

[Vivek]

Hi gVCFtools team,

We generate a single VCF file for each of genome samples  from our pipeline by merging outputs from various various detection applications such as GATK, CNVator, breakdancer and pindel. My requirement is to convert the VCF file to gVCF format for storing the variants and non-variants data in our system.

Does gVCFtool has any utility that takes a VCF file (variant data) and  BAM file(alignment data) to generate gVCF file?

Thanks,
Vivek

[Saunders, Chris]

Hi Vivek,

I don't have any recommendations for combining large-scale variant calls into a single set of records with SNVs and indels, this would tend to push against the design limits of VCF (see for instance the discussion here: https://sites.google.com/site/gvcftools/home/faq#TOC-Why-are-records-reported-in-the-gVCF-inside-of-homozygous-and-heterozygous-indels-).

For the smaller calls, if you're getting these from GATK you could try the new gVCF output mode introduced in GATK 2.7 or transfer the GATK method we describe here (https://sites.google.com/site/gvcftools/home/configuration-and-analysis/gatk_to_gvcf-usage) to an older GATK version.

Best,

-Chris

---

From: gvcftool...@googlegroups.com [gvcftool...@googlegroups.com] on behalf of Vivek [vivekg...@gmail.com]
Sent: Tuesday, November 26, 2013 8:56 AM
To: gvcftool...@googlegroups.com
Subject: VCF to gVCF conversion