IGV supporting CRAM 3.1 ?

[Yvan Wenger]

Hello, is IGV supporting CRAM 3.1 in certain conditions ? In my hands not, but still wondering because CRAMs can come in many flavours ; my CRAM might just miss some content required by IGV. It was generated using:

samtools view -C -T genom_ref.fa  -o embed_ref_3.1.cram -@ 10 -O cram,version=3.1,embed_ref=1 100mio_reads.bam

Many thanks !

Yvan

[igv-help]

Hi, thanks for sending the test file.   At this time IGV does not support CRAM version 3.1.

[Jerry Liu]

Any estimate of when IGV will support CRAM v3.1? We have switched to 3.1 for its higher compression ratio.

Thanks!

Jerry

[James Robinson]

As soon as the htsjdk supports it (https://github.com/samtools/htsjdk/pull/1714) we will do a release.  They are working on it, the last estimate I got was the end of the year.

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[Jerry Liu]

Hi James,

Thanks very much for the update. We have converted all archived BAMs to CRAM v3.1, and this is really great news for us :) We look forward to the release!

Best,

Jerry