Retrieving alignment scores with vg surject

Question

[Gabriela]

Hello!

I'm trying to get multiple alignments with their corresponding alignment scores for paired-end reads against a pangenome using vg giraffe, and then vg surject to convert gam to bam. As result, the generated bam file contains multiple alignments for paired-end reads but alignment scores AS:XX are not reported. Is there an option for including them in the alignment section of sam/*bam files?

For generating pangenome alignments I'm using the following command line:

vg giraffe -M 10 -x ${panIdxPath}/${panPre}.xg -g ${panIdxPath}/${panPre}.gg -H ${panIdxPath}/${panPre}.gbwt \
-L 2000 -m ${panIdxPath}/${panPre}.min -d ${panIdxPath}/${panPre}.dist -p -f ${fastq1} -f ${fastq2} -t 30 \
1> ${outPre}.gam --report-name ${log} 2> ${log}_run.log

For converting the gam file to bam file, I'm running:

vg surject -b -M -i -t 30 -x ${panIdxPath}/${panPre}.xg ${prefix}.gam 1> ${prefix}.bam

Thanks,

Gabriela

[Jordan M Eizenga]

I believe that option does not currently exist, but you could make a feature request on our GitHub issues: https://github.com/vgteam/vg/issues

[Gabriela]

Hi Jordan.

Thanks for your quick response. I'll do the request on GitHub.