Add check for reference.dict file required for HaplotypeCaller

[ChaochihL]

If you're filling this out for a bug in the code, please include the following information:

• The handler that's giving you an issue

HaplotypeCaller

- The error message

##### ERROR MESSAGE: Fasta dict file /panfs/roc/groups/9/morrellp/vonde026/Workshop/Yeast/S288C_reference_genome_R64-2-1_20150113/S288C_reference_sequence_R64-2-1_20150113.dict for reference /panfs/roc/groups/9/morrellp/vonde026/Workshop/Yeast/S288C_reference_genome_R64-2-1_20150113/S288C_reference_sequence_R64-2-1_20150113.fasta does not exist. Please see https://software.broadinstitute.org/gatk/documentation/article?id=1601 for help creating it.

- A copy of the section in your Config for the relevant handler

#   What are our Qsub settings for Haplotype_Caller?
#       Below are the recommended settings
HC_QSUB="mem=250gb,nodes=1:ppn=24,walltime=24:00:00"

#   Which queue are we submitting the job to?
HC_QUEUE="ram256g"

#   Where is the list of finished BAM files?
#       To generate this list, use sample_list_generator.sh
#       located at /sequence_handling/HelperScripts/sample_list_generator.sh
FINISHED_BAM_LIST=/panfs/roc/groups/9/morrellp/vonde026/Workshop/Yeast/SAM_Processing/SAMtools/Yeast_Sample_BAM.txt

#   What is the nucleotide diversity per base pair (Watterson's theta)?
#       For barley: 0.008
#       For soybean: 0.001
THETA=0.005

- A copy of the dependencies section in your Config

- Here is a link to code that will create the reference.dict file. I have run the script and it works.

Code link: fasta_seq_dict.job

[Aerin13]

This issue was fixed in the latest commit. All GATK handlers should now check for a reference.dict and generate one if it does not exist. Thank you for pointing this out.