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Alt contigs? #72

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bwlang opened this issue Jan 20, 2017 · 1 comment
Open

Alt contigs? #72

bwlang opened this issue Jan 20, 2017 · 1 comment

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@bwlang
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bwlang commented Jan 20, 2017

I searched a bit but did not find any documentation about how to use bowtie2 with alt alleles in grch38. Are there recommendations about to handle these?
@BenLangmead
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Bowtie 2 doesn't currently consider alt loci as such while aligning. This is very much on the TODO list. In the meantime, we recommend people use the "primary" assembly with Bowtie 2.

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@bwlang @BenLangmead