Fixes for VCF version 4.3. in single and paired mode - Githubissues

AstraZeneca-NGS / VarDict

VarDict

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Fixes for VCF version 4.3. in single and paired mode #117

Closed PolinaBevad closed 5 years ago

PolinaBevad commented 5 years ago

Description

This PR fixes several errors that appear while validating VCF files with vcf-tools validator and EBI-Variation validator.

For paired VCF:

Updated BIAS fields (must be Number=2) and SOR field (will be 0 in case of Inf).
Added reference and contig tags options.
Added check for MSI filter duplication.
MQ field now is Integer in FORMAT info, as in specification.
AF is Number=A now.

For single VCF:

Added reference tag option.