alignment-nf

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Re-evaluate SAM/BAM processing tools

1

Check which tools among samblaster sambamba biobambam samtools elPrep etc. is the most efficient as things might have changed a bit in the last years. See this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504710/

mfoll

When quality scores are modified during BQSR and original values are preserved (see #26), we can retrieve them (`-O` in `samtools`). This should be an option.

mfoll

mfoll

From GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360037055712-ApplyBQSR > Emit original base qualities under the OQ tag > The tool is capable of writing out the original quality scores of each read in the recalibrated...

mfoll

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1688-1

mfoll

It would be interesting to be able to input only one single fastq (no paired fastqs)

V-Catherine