first commit of run-pbwt-reference-impute
Merge branch 'develop' of vr-login:/software/vertres/git/origin/vr-codebase into develop
sga calling scripts as run for 1000G
glia+freebayes integration as run for 1000G Phase3
beagle+shapeit+mvncall runner scripts as for 1000G Phase3
updates to the run-pbwt-reference-impute runner pipeline
minor change so that gerp will work with with bed files created before and after the fix in f19ab2133fa1a7c71d0a3a592e719e5ed602dd6e
upload to dcc using aspera (as for 1000G)
vqsr scripts as for uk10k
run-chunkify: bugfix. site chunking from vcf_sites key not chunk_sites
vcf-summary: update to include MAC, HWE and Inbreeding coefficient
bcftools not happy with original COHORT header lines