From e9d53184266c9dfd0ab6d9f013d86f97f6292791 Mon Sep 17 00:00:00 2001
From: Feiyu Du <fdu@wustl.edu>
Date: Sun, 30 Jul 2023 21:38:39 -0500
Subject: [PATCH] CRAM not BAM

---
 Soma.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Soma.wdl b/Soma.wdl
index f1af01b..cd718c8 100644
--- a/Soma.wdl
+++ b/Soma.wdl
@@ -253,7 +253,7 @@ task dragen_align {
          --vc-combine-phased-variants-distance 3 --vc-enable-orientation-bias-filter true \
          --qc-coverage-ignore-overlaps=true --qc-coverage-region-1 ${CoverageBed} --qc-coverage-reports-1 cov_report \
          --qc-coverage-region-1-thresholds ${CovLevels} \
-         --intermediate-results-dir ${LocalAlignDir} --output-dir ${DragenOutdir} --output-file-prefix ${Name} --output-format BAM
+         --intermediate-results-dir ${LocalAlignDir} --output-dir ${DragenOutdir} --output-file-prefix ${Name} --output-format CRAM
      }
 
      runtime {