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ENA cram processing tools

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Typical cramtools usage in processing:

  • cram dump: java -XX:+UseSerialGC -Xmx10G -Dsamjdk.use_cram_ref_download=true -Djava.io.tmpdir="/var/tmp" -jar cramtools.jar fastq --reverse --gzip $@
  • cram stats: java -XX:+UseSerialGC -Xmx4G -cp cramtools.jar net.sf.cram.CramTools bam -c -F 2304 -I $@