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Use same sort order as Samtools #796

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almussel opened this issue Aug 21, 2015 · 2 comments
Closed

Use same sort order as Samtools #796

almussel opened this issue Aug 21, 2015 · 2 comments

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@almussel
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ADAM sorts by reference purely lexicographically, which puts unmapped reads at the beginning and mixes up chromosome order. Samtools sorts using the reference order specified in the header puts unmapped reads at the end. There are also some other subtleties that I don't know the specifics of.
@fnothaft
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Just to connect the tickets, fixing this would fix one of the three issues in #794.

@fnothaft
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fnothaft commented Jul 6, 2016

Closed by #1045.

@fnothaft fnothaft closed this as completed Jul 6, 2016
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@fnothaft @almussel