Questions about read alignment in GAM and BAM format

[b524198065]

Dear developers:

Hello and recently I was using VG to make a variant graph of a plant species and I want to compare the number of reads of one accession mapped onto the graph-based genome via vg giraffe and the linear reference genome via bwa-mem.

The read mapping statistics of bwa-mem was compute by samtools flagstat. However, when I use -o GAM and -o BAM parameters in vg giraffe mapping tools and use vg stats -a *.gam and samtools flagstat *bam, they returned different statistics regrading total alignments, total mapped reads, etc. How can I make a sensible statistics about read mapping using the graph-based genome?

Appreciated, Hongbo