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Steven-N-Hart / vcf-miner

VCF-Miner: A graphical user interface for sorting, filtering and querying annotated VCF Files
MIT License
37 stars 11 forks source link

VCF miner doesn't look like it is compatible with VCF 4.2 #18

Open Wixaros opened 6 years ago

Wixaros commented 6 years ago

Hi, I'm getting some errors with VCF miner and version 4.2 which is the format our recent files has been delivered in. Specifically this error:

WARNING: The following header line appears to have a problem: ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> Invalid value for Number=R WARNING: The following header line appears to have a problem: ##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele"> Invalid value for Number=R WARNING: The following header line appears to have a problem: ##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">

It looks like it's the new 4.2 format that has introduced R as a number. Is there a fix for this?

Best

Nicolai

Steven-N-Hart commented 6 years ago

Is it error-ing out, or just providing a warning?