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chapmanb / bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure
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using standalone tool on ICGC data. #32

Closed mortunco closed 8 years ago

mortunco commented 8 years ago

Hi Brad;

I would like to know if I can use this standalone software on VCF called algorithms other than (vardict, freebayes, mutect, varscan) ? My VCF belong to the same version 4.0.

My aim is to find consensus regions of vcf obtained from ICGC. In ICGC there are 3 vcf type which belong to 3 centers. Right now I have vcfs from Sanger and DKFZ/EMBL called by different algorithms such as caveman, platypus, pindel, delly. ( for different purposes of course (indel or snv)).

Will this software work on my case?

Best regards,

Tunc.

chapmanb commented 8 years ago

Tunc; In general the tools should work on other VCF callers. I'd suggest using the new simpler ensemble caller rather than this version:

https://github.com/chapmanb/bcbio.variation.recall#ensemble

If there are VCF validation issues or other problems you may have to handle those prior to feeding into the tools. Hope this helps.