Comments (1)
this bug seems to be fixed in picard release 3.2.0 which fix a bug related to CRAM files
from nf-resequencing-mem.
Related Issues (20)
- :zap: split chromosome relying on BAM size while running freebayes
- :bookmark: release this pipeline to the public
- :zap: call freebayes in different processes
- :bug: update pipeline to support latest nf-core/tools
- :sparkles: check that reads IDs are unique
- :arrow_up: upgrade module dependencies and test for `-stub` option
- :sparkles: use MultiQC with all supported tools
- :fire: can samtools/index be removed
- :zap: Add RG in alignment step
- :construction_worker: update CI system
- :sparkles: Annotate VCF file with SnpEff
- :wrench: configure MultiQC analysis
- :arrow_up: upgrade modules
- :heavy_plus_sign: switch to nf-validation plugin
- :zap: replace `picard/markduplicates` with `sambamba/markdup` HOT 1
- :zap: replace `picard/markduplicates` with `samtools/markdup`
- :zap: replace `bwa` with `bwa-mem2` modules
- :zap: optimize `samtools/depth` step
- :boom: add vcfallelicprimitive step
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from nf-resequencing-mem.