Using CRAM files instead of BAM files

jandrewrfarrell / RUFUS

RUFUS k-mer based genomic variant detection

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Using CRAM files instead of BAM files #21

Closed mkohailan closed 3 years ago

mkohailan commented 3 years ago

Hi,

Is there anyway to use CRAM files instead of BAM files?

This is the code I am running: runRufus.sh -s Child.bam -c Dad.bam Mom.bam Sibling1.bam Sibling2.bam Sibling(etc).bam -k 25 -t 40 -r ref.fa

Piping the output of a CRAM-to-BAM conversion tool (e.g. SAMtools view) may not be possible as I have multiple BAM files that are used in different positions of the code (i.e. 1 BAM for -s and multiple BAMs for -c)

Appreciate your help

Thanks

jandrewrfarrell commented 3 years ago

Yes, Rufus is designed to work with cram files. You pass them in just like a bam but you must also use the command line option -cr to pass in the reference used to make the cram files.