Wheat RefSeq_v1
Setup
- get jar files from Buckler Lab (phg.jar and sTASSEL.jar)
- build image
Pipeline
LoadGenomeIntervals.sh
- TASSEL requires 50G for this assembly, add Xmx=50G to configSQLite.txt
LoadAssemblyAnchors.sh - do not use, it is being rewritten
CreateHaplotypes.sh
- change gatk-launch to gatk
- fix arguments
- index documents - https://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference
- intervals.bed - change contigs from 1A to chr1A and so on
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