Wheat RefSeq_v1

Setup

  1. get jar files from Buckler Lab (phg.jar and sTASSEL.jar)
  2. edit scripts/LoadGenomeIntervals.sh to change Xmx=50G
  3. build image
  4. create BED file from high confidence genes

Pipeline

  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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