Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject
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3 months ago
cassiwatt • 0


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

giraffe surject vg • 207 views

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