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License: GNU General Public License v3.0
Whole Exome/Whole Genome Sequencing alignment pipeline
License: GNU General Public License v3.0
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 output file under the "OQ" tag. By default, this behavior is disabled because emitting original qualities results in a significant increase of the file size. Use this flag to turn on emission of original qualities.
It would be interesting to be able to input only one single fastq (no paired fastqs)
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/
I guess one only has to add a *
after the vcf
extension in these lines:
indelsvcf=`ls !{params.GATK_bundle}/*indels*.vcf
dbsnpvcfs=(`ls !{params.GATK_bundle}/*dbsnp*.vcf
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.
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