Variant_Callers_Compatible

Compatible_Variant_Callers

Somatic Variant Callers

• lancet (1.0.7)
• mutect2 (4.0.8.1)
• octopus (0.7.4 or github)
• strelka2 (2.9.10)
• vardictjava (1.6.0)
• deepsomatic (1.9.0 or up)

Germline Variant Callers [feature under development]

• deepvariant (0.8.0)
• freebayes (1.2)
• haplotypecaller (4.0.8.1)
• samtools (1.9)
• strelka2 (2.9.10)

Note: The value in parenthesis is the version of the tool from which we got the RAW VCF that was used for developing vcfMerger2 ; newer versions of these tools should work as long as their outputted VCF file has the SAME fields and/or flag required for vcfMerger2 ;
It has to be noted that even if new fields other than the vcfMerger2-FORMAT-specific TAGs or flags are added to the VCF, they will not impact vcfMerger2 functionning.

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What to do if your variant caller is not listed?

If your variant caller is not listed above, you can make their own prep script for your tool and then create a pull-request on github to ask vcfMerger2 Team to add it, or open an issue with keyword improvement as first line in bloc text and provide a full RAW VCF from your tool.

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