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CRAM Output support
We should have the possibility to output CRAM files
Issues with this:
- DeDup can't handle CRAM yet
- DamageProfiler can't handle CRAM yet
@apeltzer I think it makes more sense to close this until fixed upstream ;) and we get more requests. Thoughts?
Maybe - damageprofiler though can do cram now :)
Review of our tools that accepts CRAM format:
- [x] samtools fastq ☑️
- [x] samtools flagstat ☑️
- [x] hostremoval 🟡 (but probably easily added, as uses pysam, which does)
- [x] samtools view ☑️
- [x] dedup ❌
- [x] picard markDuplicates ☑️
- [x] bedtools ☑️
- [x] damageprofiler ☑️
- [x] mtnucratio ❌
- [x] preseq 🟡 (could just use bed format instead?)
- [x] nuclear contamination ☑️
- [x] qualimap ☑️ (not directly, but @FriederikeHanssen has made a sneaky nf-core module to make it 'supportable')
- [x] PMDTools ☑️ not natively, but uses a pipe from samtools view
- [x] BamUtils ❌
- [x] mapDamage2 🟡 (uses pysam, seemingly without particular version? Maybe work...)
- [x] GATK UnifiedGenotyper ❌
- [x] GatkHaplotypeCaller ☑️
- [x] sequenceTools ☑️
- [x] Freebayes ❌
- [x] ANGSD ☑️
So actually I guess most tools accept it, or at least there is a possible workaround...
The main blockers I would think are DeDup/MTNucRatio/UnifiedGenotyper
BamUtils I'm 99% we can find a different tool to do it for us.
Ping @apeltzer for DeDup/MTNucRatio ;)
Yeah supported, worst case I just bump the library used and it should work almost out of the box.