Fix Scramble

[vladsavelyev]

1. Drop HLA contigs from VCF to avoid:

Writing to /tmp/bcftools-sort.CBfZdQ
[W::vcf_parse] Contig 'HLA-DRB1*10' is not defined in the header. (Quick workaround: index the file with tabix.)
Error encountered while parsing the input at HLA-DRB1*10:2

HLA contig names are not well standardised, and even using the same reference build, SN:HLA-DRB1*10:01:01 in the reference genome somehow turns into HLA-DRB1*10 in a VCF. I don't think anything in GATK-SV does HLA typing, so it's safe to just drop them.

2. Add more memory to the task to avoid OOM for SCRAMble.R:

/cromwell_root/script: line 119:    19 Killed                  Rscript --vanilla $scrambleDir/cluster_analysis/bin/SCRAMble.R --out-name $clusterFile --cluster-file $clusterFile --install-dir $scrambleDir/cluster_analysis/bin --mei-refs $meiRef --ref $xDir/ref --no-vcf --eval-meis