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  • davidblaney
    replied
    I always think broads 'best practise' advice is good

    Maybe this will help: See Phase II, Section 2.



    This may be dependent on what version of GATK you are using.

    It explains how HaplotypeCaller is still experimental. I have used UnifiedGenotyper successfully but haven't tried HaplotypeCaller yet so I can't speak from experience.

    Good Luck

    Leave a comment:


  • kjaja
    started a topic calling variants using GATK

    calling variants using GATK

    Hi All,

    I was wondering about the difference between the Haplotype Caller and the Unified Genotype caller within GTAK for calling variants from exome sequencing. I know that the Haplotype Caller is slower and calls SNPs and indels att he same time but are there any advantages in using one or the other? I am looking into whether I should be using the Haplotype Caller or the Unified Genotype caller.

    Thanks,

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