Hello again. I've generated a gam (for many samples) using vg: variation graph tool, version v1.27.1 "Deliceto"
./vg map -t 16 -s $xg -g $gcsa -i -f "$R1" -f "$R2" > "$vg"_CP"$numbers"_2.gam
This command works and everything seems to be writing correctly to the .gam, but when I try to generate a vcf from the augmented graph it's completely blank. Here are the vg files' and augmented files' info (is the increase in size for augmented usual? Is that contributing to this issue, if so how much should I try to run this with?
bash-4.2$ ./vg pack -x sxab/mod_F_KS_P_RNA_scaffold_11_gfa.xg -g mod_F_KS_P_RNA_scaffold_11_gfa_CP41.gam -Q 5 -o mod_F_KS_P_RNA_scaffold_11_gfa_CP41.pack
bash-4.2$ ./vg call sxab/mod_F_KS_P_RNA_scaffold_11_gfa.xg -k mod_F_KS_P_RNA_scaffold_11_gfa_CP41.pack
bash-4.2$ ./vg call sxab/mod_F_KS_P_RNA_scaffold_11_gfa.xg -k mod_F_KS_P_RNA_scaffold_11_gfa_CP41.pack -a >> Reference_F_KS_P_RNA_scaffold_11_gfa.vcf
1.6G Jan 24 16:01 mod_F_KS_P_RNA_scaffold_11_gfa_CP41.gam
14M Jan 19 22:22 sxab/pruned_mod_F_KS_P_RNA_scaffold_11_gfa.vg
39M Jan 20 23:22 sxab/mod_F_KS_P_RNA_scaffold_11_gfa.xg
25M Jan 24 23:37 mod_F_KS_P_RNA_scaffold_11_gfa_CP41.pack
#
2.7G Jan 25 00:17 aug_mod_F_KS_P_RNA_scaffold_11_gfa_CP41.gam
1.1G Jan 25 00:20 aug_mod_F_KS_P_RNA_scaffold_11_gfa_CP41.vg
691M Jan 25 00:29 aug_mod_F_KS_P_RNA_scaffold_11_gfa_CP41.vg.xg
49M Jan 25 00:44 aug_mod_F_KS_P_RNA_scaffold_11_gfa_CP41.pack
Also, is there a way to generate a vcf with invariant regions <.> in the alt column?
