Merge pull request #73 from RoanKanninga/master

fixing coveragecalculations
molgenis · Oct 3, 2016 · e9f0b62 · e9f0b62
2 parents 57fbe0a + d8d658b
commit e9f0b62
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/protocols/CoverageCalculations.sh b/protocols/CoverageCalculations.sh
@@ -54,7 +54,7 @@ then
 
 			echo -e "Index\tChr\tChr Position Start\tDescription\tMin Counts\tCDS\tContig" > ${sampleNameID}.${perBase}.coveragePerBase.txt
 
-			awk -v OFS='\t' '{print NR,$1,$2,$5,$7,"CDS","1"}' ${sampleNameID}.${perBase}.combined_bedfile_and_samtoolsoutput.txt >> ${sampleNameID}.${perBase}.coveragePerBase.txt
+			awk -v OFS='\t' '{print NR,$1,$2,$4,$6,"CDS","1"}' ${sampleNameID}.${perBase}.combined_bedfile_and_samtoolsoutput.txt >> ${sampleNameID}.${perBase}.coveragePerBase.txt
 
 			#remove phiX
 			grep -v "NC_001422.1" ${sampleNameID}.${perBase}.coveragePerBase.txt > ${sampleNameID}.${perBase}.coveragePerBase.txt.tmp