support for CRAM files through samtools

BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

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support for CRAM files through samtools #23

Closed matthdsm closed 7 years ago

matthdsm commented 7 years ago

Hi,

Would it be possible to include support for CRAM compressed files through samtools? If I'm not mistaking, this is already native to the latest samtools/HTSlib

Cheers M

valeu commented 7 years ago

Supporting CRAM is not planned in the nearest future. Please transform you CRAM to BAM to run FREEC. Also, you can modify the code yourself to add the CRAM support and pull.