From c7b9cb2c65c39114ded82efb0c94b1110c7a052c Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Wed, 21 Jun 2023 09:35:00 +1000 Subject: [PATCH 1/3] Create copy_cram_for_str.sh --- scripts/copy_cram_for_str.sh | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 scripts/copy_cram_for_str.sh diff --git a/scripts/copy_cram_for_str.sh b/scripts/copy_cram_for_str.sh new file mode 100644 index 00000000..d172fdf4 --- /dev/null +++ b/scripts/copy_cram_for_str.sh @@ -0,0 +1,4 @@ +#!/usr/bin/env bash + +gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG3772.cram" "gs://cpg-tob-wgs-test/cram/nagim/CPG3772.cram" +gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG3772.cram.crai" "gs://cpg-tob-wgs-test/cram/nagim/CPG3772.cram.crai" From e74459774fc2903ccd2f08cd159ce2dbbcd1c911 Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Wed, 21 Jun 2023 09:40:39 +1000 Subject: [PATCH 2/3] Update copy_cram_for_str.sh --- scripts/copy_cram_for_str.sh | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/scripts/copy_cram_for_str.sh b/scripts/copy_cram_for_str.sh index d172fdf4..60171c47 100644 --- a/scripts/copy_cram_for_str.sh +++ b/scripts/copy_cram_for_str.sh @@ -1,4 +1,9 @@ #!/usr/bin/env bash +#check if segDup causing extremely high coverage gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG3772.cram" "gs://cpg-tob-wgs-test/cram/nagim/CPG3772.cram" gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG3772.cram.crai" "gs://cpg-tob-wgs-test/cram/nagim/CPG3772.cram.crai" + +# check optical duplicate issue +gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG67314.cram" "gs://cpg-tob-wgs-test/cram/nagim/CPG67314.cram" +gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG67314.cram.crai" "gs://cpg-tob-wgs-test/cram/nagim/CPG67314.cram.crai" From b8a1c5778fa030ab93e73a065cfc34b2378314eb Mon Sep 17 00:00:00 2001 From: Matt Welland Date: Wed, 21 Jun 2023 16:21:03 +1000 Subject: [PATCH 3/3] Update scripts/copy_cram_for_str.sh --- scripts/copy_cram_for_str.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/copy_cram_for_str.sh b/scripts/copy_cram_for_str.sh index 60171c47..c668fa88 100644 --- a/scripts/copy_cram_for_str.sh +++ b/scripts/copy_cram_for_str.sh @@ -7,3 +7,4 @@ gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG3772.cram.crai" "gs://cpg-tob-wgs # check optical duplicate issue gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG67314.cram" "gs://cpg-tob-wgs-test/cram/nagim/CPG67314.cram" gsutil cp "gs://cpg-tob-wgs-main/cram/nagim/CPG67314.cram.crai" "gs://cpg-tob-wgs-test/cram/nagim/CPG67314.cram.crai" +