From b817db09623580f22a49a4231c7f3def23814a27 Mon Sep 17 00:00:00 2001 From: chartl Date: Fri, 4 Dec 2009 23:29:14 +0000 Subject: [PATCH] Syzygy has a default LOD score of 0.91 on bases with no coverage, this is problematic. Set the minimum lod threshold to 1 because I just don't want to see that codswallop. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2268 348d0f76-0448-11de-a6fe-93d51630548a --- python/SyzygyCallsFileToVCF.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/SyzygyCallsFileToVCF.py b/python/SyzygyCallsFileToVCF.py index e813a6998..f23b109b0 100755 --- a/python/SyzygyCallsFileToVCF.py +++ b/python/SyzygyCallsFileToVCF.py @@ -115,7 +115,7 @@ for line in raw_calls_file.readlines(): if ( not two_lines_ago ): continue # window not filled yet else: - if ( float(this_line[lod_score_index]) > 0 and this_line[call_index] != "D" and this_line[call_index] != "I"): + if ( float(this_line[lod_score_index]) > 1 and this_line[call_index] != "D" and this_line[call_index] != "I"): # potential call chrom = this_line[chrompos].split(":")[0] pos = this_line[chrompos].split(":")[1]