Can you apply Base Score Recalibration in parallel?
Pipeline i analyse uses three steps for recalibration:
- BaseRecalibrator (in parallel)
- GatherBQSRReports
- ApplyBQSR
Is it appropriate to skip 2nd step and applyBQSR on each chunk separately with separate recal.table's ?
• 1,108 views
•
link
updated
by
LChart
•
written
by
optimistsso4co3 •
•
written
by
optimistsso4co3 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Cut&Run: E-coli spike-in
written by kim •
-
Tool: Generate unit-tested, ready-to-run pipelines using natural language prompting
written by Kevin •
-
dbSNP with RefSeq chromosome notation
written by Tom •
-
So many variants detected.
written by Mehmet
-
Reference file for base recalibration
written by priya.bmg •
-
Discussion: Clinical genetics germline variants detection pipeline
written by Jordi •
-
DNAseq pipeline steps
written by shuksi1984 •
-
GATK SNPs calling multiple sample without any known SNPs database
written by deepkumar1983 •
-
Processing Metagenomics Reads from Multiple Lanes
written by adityabandla •
-
Advice On Pre-Processing/Filtering Ngs Data
written by DonJoe •
one you have computed BaseRecalibrator , GatherBQSRReports takes only a few seconds, so there is no use in skipping that part IMHO.
Beyond that, the reports are effectively count tables; and gathering them adds the counts together. If you compute the recalibration table and apply it in the same chunk (say 1MB) then your quality scores will be horribly under-estimated, since the total number of counts will be insufficient for a score of >Q25 or so.