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allenday/kannapedia make unaligned bam.bash

Last active February 4, 2017 08:27
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kannapedia make unaligned bam.bash
for B in `ls -1 *fastq* | perl -ne 'm#^(.+?)_#;print "$1\n"' | sort | uniq`; do
echo $B;
java -jar ~/bin/picard.jar FastqToSam F1=$(ls -1 ${B}_*R1*.fastq.gz) F2=$(ls -1 ${B}_*R2*fastq.gz) O=$B.bam SAMPLE_NAME=$B;
#in case of a failure, we'll get a file of zero bytes
touch $B.bam
done;
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