Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Explain missing be tags in SvPileup #29

Merged
merged 2 commits into from
Oct 4, 2023
Merged

Explain missing be tags in SvPileup #29

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
994cece
Explain missing be tags in SvPileup
nh13 Oct 4, 2023
b37392b
Generate docs files
Oct 4, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 6 additions & 1 deletion src/main/scala/com/fulcrumgenomics/sv/tools/SvPileup.scala
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,7 +51,7 @@ object TargetBedRequirement extends FgBioEnum[TargetBedRequirement] {
|2. `<output-prefix>.bam`: a SAM/BAM file containing reads that contain SV breakpoint evidence annotated with SAM
| tag.
|
|The `be` SAM tag contains a comma-delimited list of breakpoints to which a given read belongs. Each element is
|The `be` SAM tag contains a comma-delimited list of breakpoints to which a given alignment belongs. Each element is
|a semi-colon delimited, with four fields:
|
|1. The unique breakpoint identifier (same identifier found in the tab-delimited output).
Expand All @@ -64,6 +64,11 @@ object TargetBedRequirement extends FgBioEnum[TargetBedRequirement] {
|4. The type of breakpoint evidence: either "split_read" for observations of an aligned segment of a single read
| with split alignments, or "read_pair" for observations _between_ reads in a read pair.
|
|As described in the Algorithm Overview below, split-read evidence is favored over across-read-pair evidence.
|Therefore, if the template (alignments for a read pair) contain both types of evidence, then the `be` tag
|will only be added to the split-read alignments (i.e. the primary and supplementary alignments of the read
|in the pair that has split-read evidence), and will not be found in the mate's alignment.
|
|## Example output
|
|The following shows two breakpoints:
Expand Down
Loading