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Add support for displaying SNPs in "no_ref" CRAM files #4649

Merged
merged 3 commits into from
Nov 11, 2024
Merged

Add support for displaying SNPs in "no_ref" CRAM files #4649

merged 3 commits into from
Nov 11, 2024

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cmdcolin
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@cmdcolin cmdcolin commented Nov 10, 2024

CRAM can be written as a "no_ref" file which encodes the deltas against the reference genome in the MD tag instead of the "CRAM encoded read features"

the noref files are a little larger but they are a default on galaxy

140K    volvox-sorted.cram
228K    volvox-sorted.noref.cram
388K    volvox-sorted.bam

cc @alpapan

@cmdcolin cmdcolin added the enhancement New feature or request label Nov 10, 2024
@cmdcolin cmdcolin force-pushed the noref branch 2 times, most recently from b1d7877 to 93e1086 Compare November 10, 2024 23:12
@cmdcolin cmdcolin merged commit 2f02d6b into main Nov 11, 2024
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@cmdcolin cmdcolin deleted the noref branch November 11, 2024 06:31
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