vg map, paired-end reads, multi-mapping and MAPQ

Question

[cristian.groza.mcgill]

Hi,

I have a question about how vg treats reads that are multi-mapping to different chromosomes but are then anchored to the correct location by their mate read. Normally, a multi-mapping read is assigned a MAPQ of 0. However, if vg manages to rescue the pair, will it adjust the MAPQ to be above 0 for both fragments? I know this is the case with bwa mem. I just want to make sure that the following command will not discard multi-mapping reads that are anchored to the correct location by their mate: vg filter aligned.gam -t 40 -r 0.90 -fu -m 1 -q 10 -D 999 -x index.xg > filtered.gam

Thank you in advance.