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
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
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
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