From 6587c135211b65cd3423dd90ed3d3b81114eabef Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Wed, 4 Oct 2023 14:58:25 -0700 Subject: [PATCH] Explain missing be tags in SvPileup (#29) * Explain missing be tags in SvPileup * Generate docs files --------- Co-authored-by: Nobody --- docs/tools/SvPileup.md | 7 ++++++- docs/tools/index.md | 2 +- src/main/scala/com/fulcrumgenomics/sv/tools/SvPileup.scala | 7 ++++++- 3 files changed, 13 insertions(+), 3 deletions(-) diff --git a/docs/tools/SvPileup.md b/docs/tools/SvPileup.md index fff058c..2891721 100644 --- a/docs/tools/SvPileup.md +++ b/docs/tools/SvPileup.md @@ -19,7 +19,7 @@ Two output files will be created: 2. `.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). @@ -32,6 +32,11 @@ a semi-colon delimited, with four fields: 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: diff --git a/docs/tools/index.md b/docs/tools/index.md index df8d734..349f179 100644 --- a/docs/tools/index.md +++ b/docs/tools/index.md @@ -4,7 +4,7 @@ title: fgsv tools # fgsv tools -The following tools are available in fgsv version 0.0.3-d6090a5. +The following tools are available in fgsv version 0.0.3-994cece. ## All tools All tools. diff --git a/src/main/scala/com/fulcrumgenomics/sv/tools/SvPileup.scala b/src/main/scala/com/fulcrumgenomics/sv/tools/SvPileup.scala index c036311..7e12d11 100644 --- a/src/main/scala/com/fulcrumgenomics/sv/tools/SvPileup.scala +++ b/src/main/scala/com/fulcrumgenomics/sv/tools/SvPileup.scala @@ -51,7 +51,7 @@ object TargetBedRequirement extends FgBioEnum[TargetBedRequirement] { |2. `.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). @@ -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: