BAM to FASTQ

= BAM to FASTQ =


 * 1) !/bin/bash

bam="/md1/FG_WGS/LP6005053-DNA_A02/Assembly/genome/bam/LP6005053-DNA_A02"

export tools_dir="/md2/02-applications" export samtools="${tools_dir}/samtools-0.1.6_x86_64-linux/samtools" export samtoolspath="${tools_dir}/samtools-0.1.6_x86_64-linux" export classpath=$classpath:$samtoolspath export picard="${tools_dir}/picard-tools-1.56" export classpath=$classpath:$picard export heap=8000 $samtools sort -n -m 8000000000 \ $bam.bam  \ $bam.sorted_by_name java -Xmx${heap}m \ -jar ${picard}/SamToFastq.jar \ INPUT=$bam.sorted_by_name.bam \ FASTQ=$bam.read1.fastq \ SECOND_END_FASTQ=$bam.read2.fastq \ NON_PF=true \ RE_REVERSE=true

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