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genotype check uses samtools mpileup - change to bcftools mpileup #456

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ces opened this issue Oct 3, 2017 · 0 comments
Open

genotype check uses samtools mpileup - change to bcftools mpileup #456

ces opened this issue Oct 3, 2017 · 0 comments

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@ces
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ces commented Oct 3, 2017

npg_qc::utils::bam_genotype uses samtools mpileup which apparently will soon be deprecated. Best practice is to use bcftools mpileup (http://www.htslib.org/workflow/).
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