From fbd1bc81cf7a84a04031a37ca79b149bad8ba653 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Mon, 9 May 2016 13:35:41 +0200
Subject: [PATCH] by default report the SVtype in the ALT field
---
.../lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py b/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
index 262971146..e79dd50e4 100644
--- a/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
+++ b/biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
@@ -157,7 +157,7 @@ def _format_vcffile(dictreader, vcffile, samplename):
CHROM = line['Chr1']
# TODO Figure out whether we have zero or one based positioning
POS = int(line['Pos1'])
- ALT = '.'
+ ALT = '<{}>'.format(line['Type'])
SVEND = int(line['Pos2'])
INFO = 'SVMETHOD=breakdancer;SVTYPE={}'.format(line['Type'])
--
GitLab