I'm trying to compare alignment results between mapping tools, however, I've noticed that the .sam files I've made using vg surject are missing the NM:i field. Is there a way to generate a .sam file via vg giraffe or vg surject that includes this information?
This question is very similar to, but different from, this post which seems to have been resolved on github via the developers adding the sam field to the output, making me think that NM:i is simply not included in vg surject's functionality right now?
Here are examples of the commands I'm using:
vg giraffe -p -M 10 -t 30 -Z graph_index.giraffe.gbz -m graph_index.min -d graph_index.dist -f fastq1.fastq -f fastq2.fastq -o GAM mapped_reads.gam
vg surject -s -M -i -t 30 -x graph.xg mapped_reads.gam > mapped_reads.sam
Thank you! Cassi