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Fixup usage
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tfenne committed Mar 1, 2022
1 parent 71f3bb2 commit b242d94
Showing 1 changed file with 4 additions and 13 deletions.
17 changes: 4 additions & 13 deletions src/main/scala/com/fulcrumgenomics/umi/GroupReadsByUmi.scala
Original file line number Diff line number Diff line change
Expand Up @@ -439,20 +439,11 @@ object Strategy extends FgBioEnum[Strategy] {
| 3. The assigned UMI tag
| 4. Read Name
|
|Reads are aggressively filtered out so that only high quality reads/mappings are taken forward. Single-end
|reads must have mapping quality >= `min-map-q`. Paired-end reads must both have mapping quality >= `min-mapq`
|(Note: the `MQ` tag is required on reads with mapped mates). By default, paired-end reads must have both reads
|mapped to the same chromosome (to turn off this filter, use `--allow-inter-contig`).
|During grouping, reads are filtered out if a) all reads with the same queryname are unmapped, b) any primary
|read has mapping quality < `min-map-q` (default=1), or c) the primary mappings for R1 and R1 are on different
|chromosomes and `--allow-inter-contig` has been set to false.
|
|This is done with the expectation that the next step is building consensus reads, where
|it is undesirable to either:
|
| 1. Assign reads together that are really from different source molecules
| 2. Build two groups from reads that are really from the same molecule
|
|Errors in mapping reads could lead to both and therefore are minimized.
|
|Grouping of UMIs is performed by one of three strategies:
|Grouping of UMIs is performed by one of four strategies:
|
|1. **identity**: only reads with identical UMI sequences are grouped together. This strategy
| may be useful for evaluating data, but should generally be avoided as it will
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