GenotypeSperm

[YULEITSINGTAO]

Hello there,

I am wondering if you can share the instruction about the GenotypeSperm function which call the SNP based on sperm sequencing. I appreciate your time and help in advance.

Thanks
Lei

[jamesnemesh]

Hi, It would be helpful to better understand what you need if you have a more specific question. For now, let me point to a few resources: Avery’s code and descriptions of exactly how she performed the analysis here: https://zenodo.org/record/3561080#.YO2d7G4pA8Y <https://zenodo.org/record/3561080#.YO2d7G4pA8Y> If you invoke GenotypeSperm directly, you’ll see the various arguments you can use to invoke it. You need a few bits of information: 1) A BAM file containing your read data 2) A Picard style list of intervals where you want to measure pileups on your data(https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists <https://gatk.broadinstitute.org/hc/en-us/articles/360035531852-Intervals-and-interval-lists>) 3) A list of cell barcodes that represent true cells (and not empty beads) in your experiment

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-Jim

On Jul 12, 2021, at 6:33 PM, YuLei ***@***.***> wrote: Hello there, I am wondering if you can share the instruction about the GenotypeSperm function which call the SNP based on sperm sequencing. I appreciate your time and help in advance. Thanks Lei — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#264>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZXJYJAVJYKEOLRPBDMXLTXNUUPANCNFSM5AHX2NWQ>.

[YULEITSINGTAO]

Thanks for sharing. I am working on the 1x sperm sequences and I want to call the SNP from sperm sequencing by GenotypeSperm for my downstream analysis.

Thanks
Lei

[jamesnemesh]

Closed as there was no further response.