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AstraZeneca-NGS / VarDictJava

VarDict Java port
MIT License
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Missing genotype/format fields improperly formatted #321

Closed nh13 closed 4 years ago

nh13 commented 4 years ago

Running VarDictJava through var2vcf_paired.pl, the VCF has output in the "normal" format field as ..SNV:0:0:::::0::::. The VCF spec says that all missing fields must be ., so there should be a period between colons for missing values. This precludes using tools like picard and gatk as we get:

Exception in thread "main" htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 58: There are too many keys for the sample <redacted>, keys = GT:DP:VD:ALD:RD:AD:AF:BIAS:PMEAN:PSTD:QUAL:QSTD:SBF:ODDRATIO:MQ:SN:HIAF:ADJAF:NM <redacted> <redacted>:SNV:0:0:::::0::::, values = ., for input source: <redacted>

nh13 commented 4 years ago

Closing as this looks like an issue in var2vcf_paired.pl. See: https://github.com/AstraZeneca-NGS/VarDict/issues/150