Tool to combine Germline Variant call from different variant callers

Question

[rohitsatyam102]

Hi everyone

Is there a tool to combine VCFs generated from different germline variant callers such as Lofreq, iVAR, Bcftools and haplotypecaller (maybe union or intersection) that chooses variants based on something like majority voting rule like if a variant is supported by atleast 3 or more variant callers it's gonna keep it.

I know there exists many ensembl method like SomaticCombiner for Somatic variant calling algorithms but I couldn't find anything on germline.

Answer 1

[David Langenberger]

Yes, there are several tools that you can use to combine germline variant calls generated from different variant callers, including:

1. bcftools: This is a versatile tool that can be used to combine VCF files generated by different variant callers, and also perform tasks such as merge, filter, and annotate VCF files.
2. VCFtools: This is a suite of command-line tools for working with VCF files, and it includes a tool called vcf-isec that can be used to identify overlapping variants in multiple VCF files, and merge them based on different criteria.
3. CombineVariants from GATK: This tool is part of the Genome Analysis Toolkit (GATK) and is used to merge and merge and combine variant calls from different sources into a single file.
4. JAMM: This is a Java-based tool for merging and evaluating variant calls from multiple callers, and it allows you to set custom filtering rules based on different criteria.

It is important to keep in mind that combining variant calls from multiple callers can introduce both false positive and false negative variants, so careful evaluation and interpretation of the results is essential.

[rohitsatyam102]

Hi David Langenberger

I have been using bcftools but I don't know how to get like a proportion value of how many variant callers support a particular variant (like 50% of variant callers support this particular variant).

Will definitely check out CombineVariants.

I couldn't find the JAMM, can you please share the link of paper/github?

[rohitsatyam102]

I am afraid CombineVariants is not available anymore as per discussion thread here