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kevin3/extract-unmapped-reads-bam.sh

Created July 15, 2021 14:29
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extract-unmapped-reads-bam.sh
#!/bin/bash
samtools view -b -f 4 $1 > $1.unmapped.bam
samtools index $1.unmapped.bam
java -Xmx8g -jar /opt/picard/picard-tools-current/picard.jar SamToFastq I=$1.unmapped.bam F=$1.unmapped.bam.fastq
/home/ionadmin/bin/bbmap/reformat.sh in=$1.unmapped.bam.fastq out=$1.unmapped.bam.fastq.fasta
gzip $1.unmapped.bam.fastq.fasta
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