I am currently using vgtools on ancient DNA. My objective is to map reads to the variation graph and call variants using vg. In the past, I used bwa to do the alignments, and remove duplicates (Markduplicates) and calibrate PMD (MapDamage) on the BAM file. However, in the vg workflow, I put in two paired FASTQ file to do the mapping, and then I got a GAM file. I haven't figure out a way to put GAM into further modification.
Any suggestions on dealing with duplicates and PMD using vg?