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Fix an error in the bam-readcount intructions
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susannasiebert committed Sep 29, 2016
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Expand Up @@ -67,7 +67,7 @@ pVAC-Seq optionally accepts bam-readcount files as inputs to add coverage inform

Follow the installation instructions on the `bam-readcount GitHub page <https://github.com/genome/bam-readcount#build-instructions>`_.

bam-readcount uses a bam file as input, and the bam may either contain snvs or indels. Indel bams must be run in a special insertion-centric mode. Any mixed input bams must be split into snvs and indels, and bam-reacount must then be run on each file individually.
bam-readcount uses a bam file and regions file as input, and the bam regions may either contain snvs or indels. Indel regions must be run in a special insertion-centric mode. Any mixed input regions must be split into snvs and indels, and bam-reacount must then be run on each file individually using the same bam.

**Example bam-readcount command**

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