Indexing genomes for srma

• install Picardtools: basically, this is extracting the *.jar files to an appropriate place.
• install samtools

general

java -jar /path/to/CreateSequenceDictionary.jar R=<referencefile.fasta> O=<referencefile.dict>

1. java -jar /opt/picardtools/CreateSequenceDictionary.jar R=build37_chr21.fa O=build37_chr21.dict
2. Install samtools, and index the genome also according to Indexing genomes for samtools.