SV reports: add in read depth and alt allele depth (and maybe genotype)

[Madelinehazel]

Our BND reports have columns denoting depth, as well as the reads supporting the alternate allele and reference allele, but our SV reports do not. In order to add this information, you will have to pull it from the metaSV VCF:

##INFO=<ID=NORMAL_COUNT,Number=1,Type=Integer,Description="Number of normal reads supporting reference">
##INFO=<ID=NUM_READS,Number=1,Type=Integer,Description="Number of reads supporting event">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">

You will have to pull this information for each sample and integrate that code in the SVGrouper code. This script pulls in the metaSV VCF for each family member and extracts the variants, grouping them by reciprocal overlap. This will result in three new columns for each sample, e.g:

family_sample1_REF_DEPTH, family_sample1_ALT_DEPTH, family_sample1_DEPTH
family_sample2_REF_DEPTH, family_sample2_ALT_DEPTH, family_sample2_DEPTH
family_sample3_REF_DEPTH, family_sample3_ALT_DEPTH, family_sample3_DEPTH