diff --git a/bin/compareWithVKGL_gatk4_b38.sh b/bin/compareWithVKGL_gatk4_b38.sh index 6f39b8f..e86aa54 100755 --- a/bin/compareWithVKGL_gatk4_b38.sh +++ b/bin/compareWithVKGL_gatk4_b38.sh @@ -10,14 +10,14 @@ function showHelp() { # cat <20\tsummedDP\ttargetSize\tnumberBasesDPInCategoryLow\tnumberBasesZeroCoverage" + "\n" )) + ohandle.write(str("chr\tstart\tstop\tgene\tGQ_low\tGQ_medium\tGQ_high\tavgDp\tpercentage DP<10\tpercentage DP>10\tsummedDP\ttargetSize\tnumberBasesDPInCategoryLow\tnumberBasesZeroCoverage" + "\n" )) with open(bed)as f: for line in f: content= line.strip().split() @@ -223,7 +223,7 @@ def main(): global dictGQThresholds global dictDPThresholds dictGQThresholds = {'low': 20, 'medium': 50, 'high': 50} - dictDPThresholds = {'low': 20} + dictDPThresholds = {'low': 10} parser = argparse.ArgumentParser(description=desc) @@ -238,8 +238,8 @@ def main(): parser.add_argument("-q", "--qualityThresholds", type=list, default=[20,50], help="Genotype quality range per category low, medium, high. default: [20,50]" "This results in GQ categories: low: 0 <-> 20, medium: 21 <-> 50, high: > 51") - parser.add_argument("-d", "--depthThresholds", type=list, default=[20], - help="DepthThreshold, default=[20] this results in GQ categories: low: 0 <-> 20,high: > 20") + parser.add_argument("-d", "--depthThresholds", type=list, default=[10], + help="DepthThreshold, default=[10] this results in GQ categories: low: 0 <-> 10,high: > 10") parser.add_argument("-b", "--bedfile", type=str,required=True,help="target bedfile to calculate percentage per quality threshold." "Bedfile must contain colunms: chr \t start \t stop \t gene") parser.add_argument("-g", "--bedgraph", type=bool, default=True, diff --git a/bin/tortilla.sh b/bin/tortilla.sh index d135bf0..c8e68fe 100755 --- a/bin/tortilla.sh +++ b/bin/tortilla.sh @@ -9,17 +9,18 @@ cat <