handle about the GATKHardSNP in VCF header

[hmkim]

SyntaxError: One of the FILTER lines is malformed: ##FILTER=<ID=GATKHardSNP,Description="Set if true: TYPE=\"snp\" && (MQ < 30.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || QD < 2.0 || FS > 60.0)">

Can I handle this type of header in vcf file?

[moonso]

Hi,

that is a malformed VCF header line, you can check the specification here: https://samtools.github.io/hts-specs/VCFv4.2.pdf

So for this case:

1.2.2 Information field format INFO fields should be described as follows (first four keys are required, source and version are recommended):

INFO<ID=ID,Number=number,Type=type,Description="description",Source="source",Version="version">

So you could either delete that line or update it to the correct format.

Regards,

Måns

[hmkim]

Ok, I see

Thank you!