modified: cre.bam.validate.sh

new file: cre.bam_recovery.sh
naumenko-sa · Aug 22, 2017 · d0a59ba · d0a59ba
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diff --git a/cre.bam.validate.sh b/cre.bam.validate.sh
@@ -7,6 +7,7 @@
 
 # thorough validation:
 # https://gatkforums.broadinstitute.org/gatk/discussion/7571/errors-in-sam-bam-files-can-be-diagnosed-with-validatesamfile
+# bam recovery: http://genome.sph.umich.edu/wiki/BamUtil:_convert#BAM_File_Recovery
 
 if [ -z $bam ]
 then

diff --git a/cre.bam_recovery.sh b/cre.bam_recovery.sh
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+#PBS -l walltime=5:00:00,nodes=1:ppn=1
+#PBS -joe .
+#PBS -d .
+#PBS -l vmem=20g,mem=20g
+
+#http://genome.sph.umich.edu/wiki/BamUtil:_convert#BAM_File_Recovery
+
+bam convert --recover --in $bam --out `echo $bam | sed s/bam/recovered.bam/`