I'm struggling with making VarScan's output adhere to GATK's strict rules for VCF files. Currently, I cannot understand what is wrong with this line:
1 20571284 . CAAAAAAA,AAAAAAAA C .
GATK says this cannot be parsed. Are two reference alleles not allowed, or is is supposed to be formatted otherwise?
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written
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philip.jonsson •
No the VCF spec says that there is only one REF allele: http://samtools.github.io/hts-specs/VCFv4.2.pdf while you can have one or more ALT bases
REF - reference base(s): Each base must be one of A,C,G,T,N (case insensitive). Multiple bases are permitted.
ALT: Comma separated list of alternate non-reference alleles called on at least one of the samples.
to solve your problem, you can duplicate your VCF line:
1 20571284 . AAAAAAAA C .
1 20571284 . CAAAAAAA C .
but (as said Heng below) you'll also have to check the following statement of the spec: (REF) "Strings must include the base before the event"
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written
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Pierre Lindenbaum
Alright, thank you. I suspected that was the case but didn't find anything that verified it.
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EDIT: OK, what is the reference base at 20571284? Is it C or A or M or N?