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One sample analysis with HaplotypeCaller

JulsJuls Member ✭✭
edited July 10 in Ask the GATK team

Hi,

I was wondering if this will give the same results for a ONE sample analysis:

A ) HaplotypeCaller in GVCF mode and then GenotypeGVCFs to get a normal vcf file instead of the g.vcf for just the one sample
and
B ) HaplotypeCaller in normal mode for just the one sample

Which one is the recommended route for a one sample analysis?

Thank you for your help!!!

Best Answer

  • bshifawbshifaw admin
    Accepted Answer

    The results for both should be the same. If you would like to process one sample you're better off with method B. However if you have several samples that need to be processed then its suggested to use method A which works very efficiently with large sets of samples. More details here.

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin
    Accepted Answer

    The results for both should be the same. If you would like to process one sample you're better off with method B. However if you have several samples that need to be processed then its suggested to use method A which works very efficiently with large sets of samples. More details here.

  • JulsJuls Member ✭✭

    Thank so much for your help!

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