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1. LoadGenomeIntervals.sh

   1. TASSEL requires 50G for this assembly, add Xmx=50G to configSQLite.txt

2. LoadAssemblyAnchors.sh - do not use, it is being rewritten

3. CreateHaplotypes.sh

   1. change gatk-launch to gatk
   2. fix arguments
   3. index documents - https://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference

      1. java -jar picard.jar CreateSequenceDictionary R=/data2/sra/161010_Chinese_Spring_v1.0_pseudomolecules.fasta
         java -jar picard.jar CreateSequenceDictionary R=tmpFileDir/data/reference/161010_Chinese_Spring_v1.0_pseudomolecules.fasta
         samtools faidx 161010_Chinese_Spring_v1.0_pseudomolecules.fasta

   4. intervals.bed - change contigs from 1A to chr1A and so on

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