specify bam index path

broadinstitute · Jun 13, 2024 · 27c95c1 · 27c95c1
1 parent de27b97
commit 27c95c1
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/CoverageProfiler/CoverageProfiler.wdl b/CoverageProfiler/CoverageProfiler.wdl
@@ -58,6 +58,7 @@ workflow coverageProfile {
         gatk --java-options "-Xmx~{command_mem_mb}m" DepthOfCoverage \
             -L ~{intervals} \
             --input input/~{sampleName}.bam \
+            --read-index input/~{sampleName}.bam.bai \
             --reference ~{referenceFasta} \
             --output output/~{sampleName}