From 11ee83e10118f7408084557c432af64de6e044ed Mon Sep 17 00:00:00 2001 From: tobiasrausch Date: Fri, 13 Nov 2020 13:24:55 +0100 Subject: [PATCH] BND table --- README.md | 42 ++++++++++++++++++++++++++---------------- src/util.h | 4 ++-- 2 files changed, 28 insertions(+), 18 deletions(-) diff --git a/README.md b/README.md index 785e090..216b5f9 100644 --- a/README.md +++ b/README.md @@ -73,22 +73,32 @@ Gene and SV annotation can be run in a single command. Using [delly](https://github.com/dellytools/delly) and the `INFO/CT` values one can identify gene fusion candidates. Here is the mapping from gene strand to CT values with classical cancer genomics examples (GRCh37 coordinates). -| chr | start | chr2 | end | svtype | ct | startfeature | endfeature | -|------|----------|------|-----------|--------|------|--------------|--------------| -| chrA | posStart | chrA | posEnd | DEL | 3to5 | geneA(0;+) | geneB(0;+) | -| chrA | posStart | chrA | posEnd | DEL | 3to5 | geneC(0;-) | geneD(0;-) | -| 21 | 39887792 | 21 | 42869743 | DEL | 3to5 | ERG(0;-) | TMPRSS2(0;-) | -| chrA | posA | chrB | posB | BND | 3to3 | geneA(0;+) | geneB(0;-) | -| chrA | posA | chrB | posB | BND | 3to3 | geneC(0;-) | geneD(0;+) | -| chrA | posA | chrB | posB | BND | 3to5 | geneA(0;+) | geneB(0;+) | -| chrA | posA | chrB | posB | BND | 3to5 | geneC(0;-) | geneD(0;-) | -| 21 | 42867595 | 7 | 14027003 | BND | 3to5 | TMPRSS2(0;-) | ETV1(0;-) | -| chrA | posA | chrB | posB | BND | 5to5 | geneA(0;+) | geneB(0;-) | -| chrA | posA | chrB | posB | BND | 5to5 | geneC(0;-) | geneD(0;+) | -| chrA | posA | chrB | posB | BND | 5to3 | geneA(0;+) | geneB(0;+) | -| chrA | posA | chrB | posB | BND | 5to3 | geneC(0;-) | geneD(0;-) | -| 21 | 39826990 | 1 | 205637229 | BND | 5to3 | ERG(0;-) | SLC45A3(0;-) | - +| chr | start | chr2 | end | svtype | ct | startfeature | endfeature | +|------|-----------|------|-----------|--------|------|---------------|---------------| +| chrA | posStart | chrA | posEnd | INV | 3to3 | geneA(0;+) | geneB(0;-) | +| chrA | posStart | chrA | posEnd | INV | 3to3 | geneC(0;-) | geneD(0;+) | +| 10 | 89672219 | 10 | 90267336 | INV | 3to3 | PTEN(0;+) | RNLS(0;-) | +| chrA | posStart | chrA | posEnd | DEL | 3to5 | geneA(0;+) | geneB(0;+) | +| chrA | posStart | chrA | posEnd | DEL | 3to5 | geneC(0;-) | geneD(0;-) | +| 21 | 39887792 | 21 | 42869743 | DEL | 3to5 | ERG(0;-) | TMPRSS2(0;-) | +| chrA | posStart | chrA | posEnd | DUP | 5to3 | geneA(0;+) | geneB(0;+) | +| chrA | posStart | chrA | posEnd | DUP | 5to3 | geneC(0;-) | geneD(0;-) | +| 7 | 138547350 | 7 | 140491430 | DUP | 5to3 | KIAA1549(0;-) | BRAF(0;-) | +| chrA | posStart | chrA | posEnd | INV | 5to5 | geneA(0;+) | geneB(0;-) | +| chrA | posStart | chrA | posEnd | INV | 5to5 | geneC(0;-) | geneD(0;+) | +| 8 | 32139712 | 8 | 33359541 | INV | 5to5 | NRG1(0;+) | TTI2(0;-) | +| chrA | posA | chrB | posB | BND | 3to3 | geneA(0;+) | geneB(0;-) | +| chrA | posA | chrB | posB | BND | 3to3 | geneC(0;-) | geneD(0;+) | +| 14 | 68316364 | 5 | 58914908 | BND | 3to3 | RAD51B(0;+) | PDE4D(0;-) | +| chrA | posA | chrB | posB | BND | 3to5 | geneA(0;+) | geneB(0;+) | +| chrA | posA | chrB | posB | BND | 3to5 | geneC(0;-) | geneD(0;-) | +| 21 | 42867595 | 7 | 14027003 | BND | 3to5 | TMPRSS2(0;-) | ETV1(0;-) | +| chrA | posA | chrB | posB | BND | 5to3 | geneA(0;+) | geneB(0;+) | +| chrA | posA | chrB | posB | BND | 5to3 | geneC(0;-) | geneD(0;-) | +| 21 | 39826990 | 1 | 205637229 | BND | 5to3 | ERG(0;-) | SLC45A3(0;-) | +| chrA | posA | chrB | posB | BND | 5to5 | geneA(0;+) | geneB(0;-) | +| chrA | posA | chrB | posB | BND | 5to5 | geneC(0;-) | geneD(0;+) | +| 3 | 169190498 | 2 | 47689038 | BND | 5to5 | MECOM(0;-) | MSH2(0;+) | ## Citation diff --git a/src/util.h b/src/util.h index 3401ceb..120e196 100644 --- a/src/util.h +++ b/src/util.h @@ -169,7 +169,7 @@ namespace sansa inline int32_t deriveEndPos(bcf1_t* rec, std::string const& svtval, int32_t const pos2val, int32_t const endval) { if ((pos2val != -1) && (endval != -1)) { - if (svtval == "BND") return pos2val; + if ((svtval == "BND") || (svtval == "TRA")) return pos2val; else return endval; } else if (pos2val != -1) return pos2val; @@ -257,7 +257,7 @@ namespace sansa // Decode Orientation inline int32_t _decodeOrientation(std::string const& value, std::string const& svt) { - if (svt == "BND") { + if ((svt == "BND") || (svt == "TRA")) { if (value=="NA") return DELLY_SVT_TRANS + 0; else if (value=="3to3") return DELLY_SVT_TRANS + 0; else if (value=="5to5") return DELLY_SVT_TRANS + 1;