Reads with name=dG both have IS_FIRST_IN_PAIR=0

[tanger-code]

Hi. I first map the paired end reads to .vg graph. Then use vg surject to convert the .gam file to .bam file. Then I use graphtyperto do genotyping. But there is an error: Reads with name=dG both have IS_FIRST_IN_PAIR=0. Why does this happen?

[hannespetur]

Hey, graphtyper expects to find 2 reads with the same read name to form a read pair. One is expected to be marked as first-in-pair and other as second-in-pair. In this case graphtyper found two reads with name "dG" that are both marked as the second-in-pair so it cannot form the read pair.

Best, Hannes