Comments (1)
Poking this.
We'd like to add read groups for clipped, split, discordant, or properly-paired unsplit not-overly-clipped mappings in order to tabulate base modifications. Excluding discordant from the "main" properly-paired not-overly-clipped mappings is easy enough. Excluding clipped reads appears to mean using a perl script but does not appear to be a showstopper. Excluding split reads is something of a showstopper unless we reach in and heavily modify Samblaster itself. I imagine this would be a more straightforward task for someone who is exceedingly familiar with Samblaster.
It looks like the commented block starting around line 350 in samblaster.cpp touches on this -- is there a timeline for read-grouping and/or UMI support? Read grouping (split/disc/clipped/otherwise-OK) appears to be on the todo list for others as well.
Thanks for a great tool.
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Related Issues (20)
- Support for DT tag to distinguish PCR and optical duplicates HOT 6
- Can not run MarkDup for very large bam file HOT 1
- remove duplicate for single-end read HOT 4
- Duplicate `MC` tags in samblaster output HOT 6
- Getting splitters BAM from long reads data? HOT 7
- Segmentation fault on getting split reads from long read file? HOT 7
- Can't find first and/or second of pair error HOT 1
- Very different result between samtools and samblaster HOT 3
- can samblaster tackle reads with UMI? HOT 1
- walltime is twice cpu seconds HOT 3
- Alpine-based docker build fails HOT 1
- unmated reads HOT 1
- Please adapt the metrics
- Pipe output to samblaster from bwa-mem2 HOT 1
- Duplicates were removed but log says 0 dups removed HOT 1
- how do samblaster define a split read? HOT 2
- Aligning in Biscuit with samblaster and samtools HOT 1
- Can't find first and/or second of pair in sam block of length HOT 1
- de-duplicating a large sam file HOT 2
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