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Make indel realignment splice aware #615

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hammer opened this issue Dec 8, 2016 · 1 comment
Open

Make indel realignment splice aware #615

hammer opened this issue Dec 8, 2016 · 1 comment

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@hammer
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hammer commented Dec 8, 2016

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@ihodes
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ihodes commented Dec 8, 2016

The GATK indel realigner errors on reads with N in the CIGAR string, or will drop them with a CLI option. At the very least, we should be able to ignore them and keep those reads in the output BAM file.

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@hammer @ihodes