To-Do: SNV pipeline - Githubissues

fpbarthel / GLASS

GLASS consortium

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To-Do: SNV pipeline #6

Closed fpbarthel closed 6 years ago

fpbarthel commented 6 years ago

SNV pipeline

[x] Mutect2 pipeline - done
[x] VarScan2

Optional

LoFreq (for tumor-only or ones with low VAF)

@sbamin can you provide callers you used for canine and a link to the flowr workflow

See https://github.com/TheJacksonLaboratory/hourglass/issues/9 and https://github.com/TheJacksonLaboratory/cgp_somatic_calls/tree/somatic_runner/flowr

fpbarthel commented 6 years ago

VarScan scatter finished for TCGA, HK, lowpass MDA and HF. VarScan gather fails for all samples with error:

cat logs/mergevarscan/TCGA-DU-6404-TP-7DHU4O.log
java.lang.IllegalArgumentException: One or more header lines must be in the header line collection

GATK issue opened here