GA/VG Pipeline Outline

## Inputs:
##   Reference: T2T-CHM13 v2.0
##   Reads: HG002 PacBio 70x Coverage, via GIAB
##   Base Variants (for vg construct): Simons Genome Diversity Project callset on T2T-CHM13 v2.0
##
## Software:
##   vg v1.47.0
##   GraphAligner v1.0.17b (bioconda)
##   cuteSV v2.0.2
##   Sniffles2 v2.0.6

## Pipeline Outline

vg construct -r $ref $variants -t 32 > $base_dir/t2t.vg

# GraphAligner and vg surject were run on subsets of reads and the BAMs were merged

GraphAligner -g $base_dir/t2t.vg -x vg -t 32 -f $reads -a $base_dir/$gam_file.gam
vg surject -x $base_dir/t2t.vg -t 32 -b $base_dir/$gam_file.gam > $work_dir/$bam_file.bam

cuteSV -t 32 --genotype --max_cluster_bias_INS 100 --diff_ratio_merging_INS 0.3 --max_cluster_bias_DEL 100 --diff_ratio_merging_DEL 0.3 --min_size 50 --min_support 5 $work_dir/$bam_file.bam $ref $dest_dir/cuteSV/$vcf_out.vcf $tmpdir

sniffles --input $work_dir/$bam_file.bam --vcf $dest_dir/sniffles/$vcf_out.vcf --reference $ref --minsupport 5 --minsvlen 50