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    Reproducing Yang et al. - Chr1 Joint Genotyping

    March 9, 2017

    Reproducing Yang et al - HaplotypeCaller

    March 8, 2017

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    March 6, 2017

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    Recent Posts

    Reproducing Yang et al. - Chr1 Joint Genotyping

    March 9, 2017

    I created a Chr1 g.vcf for both bulks. I want to see the results from joint genotyping.

    Make the Chr1 vcf:

     Then used GenotypeGVCF to genotype.

    Note the -stand_call_conf 30 option, which is performed in this step and not in the HC step (the -ERC GVCF function doesn't allo...

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