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igmmbioinformatics
trio-whole-exome
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af11f8fa
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af11f8fa
authored
3 years ago
by
ameyner2
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Update 19373_run_notes.md
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docs/run-notes/19373_run_notes.md
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af11f8fa
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@@ -166,7 +166,7 @@ time java -Xmx24g -jar ${GATK3} -T SelectVariants \
```
SOURCE_DIR=/scratch/u035/project/trio_whole_exome/analysis/output
BATCH_ID=20211005_Ansari_Morad
BATCH_NUM=2021100
6
BATCH_NUM=2021100
5
PLATE_ID=19373
PROJECT_ID=20211006_19373_438214
VERSION_N=v1
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@@ -177,7 +177,7 @@ cd /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/LOG
qsub -v SOURCE_DIR=${SOURCE_DIR}/${VERSION_N}_${BATCH_NUM},BATCH_ID=${BATCH_ID},PLATE_ID=${PLATE_ID},PROJECT_ID=${PROJECT_ID},VERSION_N=${VERSION_N},FAMILY_ID=${FAMILY_ID},DECIPHER_ID=${DECIPHER_ID} /home/u035/project/scripts/process_NHS_WES_aff_probands.sh
```
Job id 1496
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Job id 1496
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## IGV snapshots
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@@ -196,7 +196,7 @@ PLATE_ID=19373
PROJECT_ID=20211006_19373_438214
VERSION_N=v1
FAMILY_ID=438214
JOB_ID=1496
5
JOB_ID=1496
6
cd /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/LOG
mkdir /scratch/u035/project/trio_whole_exome/analysis/${PROJECT_ID}/${PLATE_ID}_${VERSION_N}_results
qsub -v PLATE_ID=${PLATE_ID},PROJECT_ID=${PROJECT_ID},VERSION_N=${VERSION_N},FAMILY_ID=${FAMILY_ID},JOB_ID=${JOB_ID} /home/u035/project/scripts/gather_NHS_WES_aff_probands_results.sh
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