CRAM 3.1 Support Status

Recent Picard and GATK release marked a milestone for CRAM 3.1 support throughout commonly used tools in bioinformatics pipeline.

HTSlib/SAMtools

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HTSlib and SAMtools have been able to read CRAM 3.1 since version 1.12, version 1.22 changes the default output CRAM version from 3.0 to 3.1.

HTSJDK

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• Read supported since: 4.3.0
• Write supported since: 5.0.0

IGV

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• Commit: igvteam/igv@81704c1
• Supported since: 2.19.5

Picard

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• Commits: broadinstitute/picard@9fed4aa, broadinstitute/picard@a53d7eb
• Supported since: 3.5.0

GATK

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• Commits: broadinstitute/gatk@312bd36, broadinstitute/gatk@54f4d9c
• Supported since: 4.7.0.0

DRAGEN

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Supported since: v4.4