From 7afd0f5ea62bd228b28d991aa79a2ed809cc6feb Mon Sep 17 00:00:00 2001 From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu> Date: Tue, 14 Jul 2020 16:43:54 -0500 Subject: [PATCH] Add unsorted deduped bam to test_data creation --- workflow/scripts/createTestData.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/workflow/scripts/createTestData.sh b/workflow/scripts/createTestData.sh index 2b76481..47c73d4 100644 --- a/workflow/scripts/createTestData.sh +++ b/workflow/scripts/createTestData.sh @@ -63,6 +63,7 @@ cp Q-Y5F6_1M.pe.alignSummary.txt ./NEW_test_data/meta/Q-Y5F6_1M.pe.alignSummary. singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.bam O=Q-Y5F6_1M.se.deduped.bam M=Q-Y5F6_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools sort -@ 20 -O BAM -o Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.deduped.bam singularity run 'docker://bicf/gudmaprbkdedup:2.0.0' samtools index -@ 20 -b Q-Y5F6_1M.se.sorted.deduped.bam Q-Y5F6_1M.se.sorted.deduped.bam.bai +cp Q-Y5F6_1M.se.deduped.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.se.deduped.bam cp Q-Y5F6_1M.se.sorted.deduped.bam ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam cp Q-Y5F6_1M.se.sorted.deduped.bam.bai ./NEW_test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.bam.bai cp Q-Y5F6_1M.se.deduped.Metrics.txt /NEW_test_data/meta/Q-Y5F6_1M.se.deduped.Metrics.txt -- GitLab