Post date: Jun 23, 2014 9:35:12 PM
The reference must include an index from samtools and a dictionary from picard. Make the dictionary like this,
java -jar ~/Source/picard-tools-1.115/CreateSequenceDictionary.jar R=mod_lg_timemaGenome.fasta O=mod_lg_timemaGenome.dict
And the index file like this,
samtools faidx mod_lg_timemaGenome.fasta