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Although I'm reading all days and nights, still confused in this area. I have hundreds of BAM files (from whole-genome sequencing of a given human population). I was wondering how I can obtain phased haplotype from raw vcf file? I read also about GATK, but didn't find a clear answer to my question. Please kindly tell me if this tool is suitable for this goal? Would you please introduce me some practical guides and pipelines that explain such an analysis step-by-step?

Thank you for your help

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  • $\begingroup$ What format are you hoping to end up with? Note that your question would be a better fit on bioinformatics.SE. $\endgroup$
    – Remi.b
    Commented May 17, 2018 at 20:57
  • $\begingroup$ Thanks. vcf file format. Sorry, what's bioinformatics.SE, is the bioinformatic forum? $\endgroup$
    – Mary
    Commented May 18, 2018 at 6:28
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    $\begingroup$ See bioinformatics.stackExchange for your future questions of the kind. $\endgroup$
    – Remi.b
    Commented May 18, 2018 at 10:28

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You should be able reformat BAM files to VCF files with PGDSpider.

I find using specific softwares for this type data formatting tends to be error prone and not practical when having a large number of files to reformat, so I personally like to simply read about the format standard and write the code to reformat myself but that's very much a matter of personal preference.

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  • $\begingroup$ Thank you for your response and forum. However, variant calling from bam file is a long story, beyond just file conversion. $\endgroup$
    – Mary
    Commented May 18, 2018 at 15:15
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You can use either HapCut2, WhatsHap or my package.

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There are multilple packages to achieve this. I have personally used bcftools (SAMtools). Here is a non exhaustive list:

  • SAMtools (bcftools);
  • VarScan2;
  • FreeBayes;
  • Platypus;
  • Deep variant
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