Indexing genomes for srma

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  • 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.