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Sex specific SNP calling from pooled sample

tanu06tanu06 CanadaMember

hi.
Can you guide me what specific parameters i should use if i want to make a sex specific SNP calling from a pooled samples of 50

Best Answer

Answers

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @tanu06
    Hi,

    I am not sure I understand your question. What exactly is your end goal? Do you have 50 diploid samples that have all been pooled together? Do you know what the sex of the samples are? Are the samples individually barcoded?

    Thanks,
    Sheila

  • tanu06tanu06 CanadaMember

    Hi Sheila,
    Thank you for been so patient.
    The 50 pooled samples have barcodes but they are both haploid and diploid. My end goal is to identify the set of SNPs coming from mother (diploid) and Father( haploid). Sorry to bother and if you find my questions vague.

    with regards,
    Tanushree

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @tanu06
    Hi Tanushree,

    I think this thread and this thread will help.

    -Sheila

  • tanu06tanu06 CanadaMember

    Thank you so much.
    But i have pooled samples having both haploid and diploid bees in that how will i mention ploidy option

    with regards,
    Tanushree

    Issue · Github
    by Sheila

    Issue Number
    1409
    State
    closed
    Last Updated
    Assignee
    Array
    Milestone
    Array
    Closed By
    vdauwera
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