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PacificBiosciences / HiPhase

Small variant, structural variant, and short tandem repeat phasing tool for PacBio HiFi reads
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possibility to utilize information from phased bam files #38

Closed WeiCSong closed 5 months ago

WeiCSong commented 5 months ago

Hi, thanks for the great tool! My samples have phased bam file (a paternal.bam and a maternal.bam file for each sample), but currently hiphase does not seems to read two bams per sample. Is there any way to utilize the phasing information of such phased bam file, or is it possible in future update? Thanks for your help.

holtjma commented 5 months ago

Hello,

I think I must be missing a key point from your description. Currently, HiPhase can accept multiple BAM files for the same sample by just specifying --bam multiple times (the sample names must match each other and the VCF).

Are you saying these BAM files have been pre-phased? As in, you want to take a phased BAM and convert that into a phased VCF? Can you describe how these BAM files were generated? I don't think I've seen a situation where BAM files were split by paternal/maternal before.

Matt

WeiCSong commented 5 months ago

just as you say, i want to input two phased bams and three vcfs for the same sample and get three phased vcf. If i input paternal and maternal bams both by --bam, will they be regarded as phased bam?

Matt Holt @.***> 于2024年6月6日周四 20:59写道：

Hello,

I think I must be missing a key point from your description. Currently, HiPhase can accept multiple BAM files for the same sample by just specifying --bam multiple times (the sample names must match each other and the VCF).

Are you saying these BAM files have been pre-phased? As in, you want to take a phased BAM and convert that into a phased VCF?

Matt

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holtjma commented 5 months ago

In its current state, HiPhase should accept those inputs and run end-to-end. However, it does not have a concept of "paternal / maternal BAM" and will simple treat each one as a BAM file (e.g., as if they were multiple runs merged together).

holtjma commented 5 months ago

Closing due to inactivity, but feel free to re-open if you have further questions.