Add CRAM file compatibility mention in README and help messages#424
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limenode wants to merge 2 commits into
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Add CRAM file compatibility mention in README and help messages#424limenode wants to merge 2 commits into
limenode wants to merge 2 commits into
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Currently the Delly README.md and the help messages within the binary do not explicitly mention CRAM file type compatibility to the user.
I made subtle changes to both the README and help messages with the goal of notifying the user of this compatibility without being overbearing by replacing every BAM file mention with a BAM/CRAM file mention.
I have confirmed with my own short-read WGS sequences (150bp reads) that
delly callanddelly cnvreturn the same outputs from either a CRAM or BAM input file derived from the same sample. This was done using the chm13v2.0_maskedY_rCRS reference sequence.Testing Methodology:
The CRAMs I used for testing were files that I generated by processing a .fastq via mapping and alignment with chm13 and duplicate marking via
GATK MarkDuplicates. The BAMs were generated by usingsamtools viewon the CRAMs with the same chm13 reference file. For thedelly cnvcall, I used the T2T-CHM13v1.1 r101 s501 mappability map as provided via https://gear-genomics.embl.de/data/delly/.I also attempted to test the files against
delly lrto see if the binary would error out when inputting a CRAM file and it seemed fine, with both the BAM and CRAM outputting nothing (as expected from passing in short-read data). As such, I decided to apply the CRAM mention to the help message fordelly lr.