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chapmanb / bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure
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error in normalized somatic calls #19

Closed parlar closed 9 years ago

parlar commented 9 years ago

I just noticed that bcbio.variation may shift position in the sample call details (somatic calls) inte the column description (#CHROM...) line of the header but not in the actual data. This caused me some headache...

chapmanb commented 9 years ago

Thanks for the report and sorry about the problem. Would you be able to provide a small example where you're seeing the issue?

parlar commented 9 years ago

I'm at ASHG, I'll provide the info as soon as practically possible. //Pär

parlar commented 9 years ago

I'll email you two vcf files (the original and one normalized). Think that's better than pasting info here. The you can test yourself also.

chapmanb commented 9 years ago

Pär; Thank you for the example file and sorry again about the issue. There was a problem when feeding multi-sample files that had not previously been run through any GATK program, so would not have had samples sorted in the GATK manner. During the prep steps files get fed into GATK's LeftAlignVariants which could sort the samples, but the next step did not grab the proper header. This resulted in the mixup issues.

I pushed a fix and a new 0.1.8 release that contains it. Sorry again for the bug and please let us know if you run into any other problems.