specify bam index location

broadinstitute · Jun 13, 2024 · de27b97 · de27b97
1 parent ed6a906
commit de27b97
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/CoverageProfiler/CoverageProfiler.wdl b/CoverageProfiler/CoverageProfiler.wdl
@@ -52,6 +52,7 @@ workflow coverageProfile {
         # Index BAM file
         gatk BuildBamIndex \
             --INPUT input/~{sampleName}.bam
+            --OUTPUT input/~{sampleName}.bam.bai
 
         # Run DepthOfCoverage
         gatk --java-options "-Xmx~{command_mem_mb}m" DepthOfCoverage \