error in normalized somatic calls

[parlar]

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]

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]

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

[parlar]

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]

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.