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Is there any parameter used for total allelic read depth with UnifiedGenotyper?

Hello!

I wanted to know whether is there any parameter which can be used with unified genotyper for alleic read depth?Like the parameters in Samtools varfilter, there are 2 parameters -d for min and -D for max read depth. So that calling SNPs can be filtered according to specific read depths.

Answers

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @bioinfo_89
    Hi,

    You can use -dcov which will downsample to a certain depth. However, this only sets a cap for the number of reads to be used. To filter on depth, you will have to wait for variant filtration step.

    -Sheila

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    @bioinfo_89 To add to @Sheila's answer, please keep in mind that filtering directly on depth is fairly crude and has some important flaws. A better way to filter based on the amount of evidence for a variant is to use QD, which is qual normalized by depth.

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