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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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Order of Tumor and Normal Sample change in vcf from different caller #1305

Closed apastore closed 8 years ago

apastore commented 8 years ago

Hi Brad, This is probably non a major Issues but, I have noticed for pair Tumor/Normal pair some caller first place the Normal and other Place the Tumor sample in the vcf.

Freebayes, Mutect2, vardict have Tumor sample at first position. GATK-HC, mutest, varscan have Normal sample as position. ensemble is inconsistent depending on samples.

Thanks! Alessandro

chapmanb commented 8 years ago

Alessandro; Thanks for asking about this. It's definitely annoying but not something we're likely to tackle in bcbio as it would require doing a lot of work re-writing VCF files. Generally it's best to assume nothing about the order of samples and to reference them based on sample names. Hopefully that works for your downstream processing.