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 $@