sample order of the freebayes vcf output

Question

[Ming Tommy Tang]

Hi,

I am testing freebayes on tumor/normal pairs. it seems no matter I put normal or tumor bam first on the command line, the sample order of the vcf is random.

tumor:F17042956987-KY290-2-WES normal: B17042956985-KY290-2-WES How does freebayes determine the order?

mutect does not maintain the order of the output vcf either https://gatkforums.broadinstitute.org/gatk/discussion/3618/ordering-of-tumor-normal-column-in-output-vcf-file

Anyone has experience on it? using freebayes v1.1.0-3-g961e5f3

Thanks, Tommy

Answer 1

[finswimmer]

Hello,

in my experiences the order is just by chance. But I didn't know whether this is a bug or a feature by freebayes.

fin swimmer

[Ming Tommy Tang]

Thank you for the info.

but I saw inside speedseq, the filtering script assumes normal comes first and then tumor. https://github.com/hall-lab/speedseq/blob/master/bin/speedseq#L156

That's what confuses me.

Tommy