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Variant discovery starting from gVCF file

Hello, as the title suggests I'm looking to use the variant discovery tools, specifically SNP discovery. However I am not starting with a FASTA or BAM file, indeed I do not currently have access to them, instead I'm starting with a gVCF file that many of the relevant commands such as haplotype caller do not accept gVCFs as input, and for those commands that do use gVCFs it is implied that they should have been produced by haplotype caller.

Best Answers

  • dbeckerdbecker Munich ✭✭✭
    edited November 2018 Accepted Answer

    Hi,

    gvcf files do contain variant calls and quality metrics for all regions, but those are already calculated by some pipeline (and caller). Even if you find a way to convert your gvcf back into a bam file, you would loose everything that makes variant calling a challenge and end up with exactly the same gvcf.
    I don't think you can recall those samples based on the gvcf files. You either have to get your hands on the bam or fastq files, or you can try to follow the best practice pipeline beginning after the Haplotypecaller and see where it leads you.

    Best,
    Daniel

    Post edited by dbecker on

Answers

  • dbeckerdbecker MunichMember ✭✭✭
    edited November 2018 Accepted Answer

    Hi,

    gvcf files do contain variant calls and quality metrics for all regions, but those are already calculated by some pipeline (and caller). Even if you find a way to convert your gvcf back into a bam file, you would loose everything that makes variant calling a challenge and end up with exactly the same gvcf.
    I don't think you can recall those samples based on the gvcf files. You either have to get your hands on the bam or fastq files, or you can try to follow the best practice pipeline beginning after the Haplotypecaller and see where it leads you.

    Best,
    Daniel

    Post edited by dbecker on
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