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No reference for samtools's benefit in stage 1 #242

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dkj opened this issue Jul 28, 2018 · 0 comments
Open

No reference for samtools's benefit in stage 1 #242

dkj opened this issue Jul 28, 2018 · 0 comments
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dkj commented Jul 28, 2018

We should be forcing reference based compression off instead of passing a reference. I understand reference-based CRAM compression is generally a bad thing if the file is not coordinate sorted (which it isn't here right?). PhiX might be different because it is so small - but think it safer just not to use a reference.

Follow-up to #241
@dkj dkj assigned dozy Jul 28, 2018
@dkj dkj changed the title No reference for scramble's benefit in stage 1 No reference for samtools's benefit in stage 1 Jul 29, 2018
dkj added a commit that referenced this issue Jul 30, 2018
@dkj
Merge pull request #243 from dozy/s2merge
bd6729f 
remove --reference flag from samtools split command

partially deals with #242
dozy pushed a commit to dozy/p4 that referenced this issue Mar 28, 2022
@kjsanger
Merge pull request wtsi-npg#242 from ces/devel
7dea509 
Add support for loading PacBio ccs secondary analysis BAM files
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