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Is there a walker that determines sex from a bam or VCF file?

apolyakapolyak State College, PA, USAMember

I have a set of bam files, and I wanted to determine the sex of the samples. My original plan was to check the zygosity of SNPs on the chrX, however is there a more reliable, automated method availible. I also tried using --sex-check in PLINK, however it hasn't been been functioning quite effectively.

Best Answer

  • tommycarstensentommycarstensen United Kingdom ✭✭✭
    edited July 2015 Accepted Answer

    @apolyak My suggestion, which is probably what you already had in mind:
    1) Call a few chromX SNPs (not PAR) from a commercial SNP array such as Illumina Omni2.5 or Affy6 using the --intervals option and an input VCF with the Omni2.5 or Affy6 chromX sites; those are for example available from the 1000G ftp.
    2) Use PLINK1.9 or bcftools1.2 (or GATK3.4?) to calculate heterozygosity.

    This should be really fast. Someone should write a tool for streamlining this process. Perhaps it already exists. Kindly let me know, if you come across such a tool. Thanks.

    EDIT: I just noticed the title of your question "from ... VCF file". PLINK1.9 can do this. What do you mean it hasn't been fucntioning quite effectively? It's slow or it doesn't give you correct results? I would plot the heterozygosities and choose thresholds, if PLINK fails to fail or pass samples. PLINK1.9 is super fast, so I suspect this is your problem.

Answers

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭
    edited July 2015 Accepted Answer

    @apolyak My suggestion, which is probably what you already had in mind:
    1) Call a few chromX SNPs (not PAR) from a commercial SNP array such as Illumina Omni2.5 or Affy6 using the --intervals option and an input VCF with the Omni2.5 or Affy6 chromX sites; those are for example available from the 1000G ftp.
    2) Use PLINK1.9 or bcftools1.2 (or GATK3.4?) to calculate heterozygosity.

    This should be really fast. Someone should write a tool for streamlining this process. Perhaps it already exists. Kindly let me know, if you come across such a tool. Thanks.

    EDIT: I just noticed the title of your question "from ... VCF file". PLINK1.9 can do this. What do you mean it hasn't been fucntioning quite effectively? It's slow or it doesn't give you correct results? I would plot the heterozygosities and choose thresholds, if PLINK fails to fail or pass samples. PLINK1.9 is super fast, so I suspect this is your problem.

  • tommycarstensentommycarstensen United KingdomMember ✭✭✭

    Perhaps check out this post:

    http://gatkforums.broadinstitute.org/discussion/6258/how-to-determine-sex-from-bam-filles
    
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