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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
This commit is contained in:
chartl 2009-12-04 23:29:14 +00:00
parent b04de77952
commit b817db0962
1 changed files with 1 additions and 1 deletions
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2
python/SyzygyCallsFileToVCF.py
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@ -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]