comparing --call output bed files with gfa file

[suyeonwy]

Hi,

I'm working on generating pangenome using 19 genome assemblies with minigraph.
After that, I generated a bed file for each used sample using the following command, and I got 19 bed files.
minigraph -cxasm --call pangenome.gfa [sample*.fa] > sample*.bed

And I noticed that there is a path (+s447539 -> +s489808) in several bed files that doesn't exist in the gfa file.
Here is the path information from two output bed files

# from sample1.bed
NC_010460.4     49562573        49562960        >s447539        >s447541        >s489808:847:+:LUXR01077659.1:1025219:1026573

# from sample2.bed
NC_010460.4       49562573        49562960        >s447539        >s447541        >s489808:847:-:AORO02009665.1:479046:480559

In this example, sample 1 and 2 had +s447539 -> +s489808 (== -s489808 -> -s447539) path, but there is no link for that path in the input gfa file
Here is the line for the corresponding path in the input gfa file that I got with 'grep' command.

$ grep "s447539" pangenome.gfa | grep "s489808"
L       s489808 -       s447539 +       0M      SR:i:18 L1:i:847        L2:i:1

And conversely, I also found that there are paths in the gfa file but not in bed files.
For example, I could find +s590861 -> -s349685 path in gfa file

grep "s590861" pangenome.gfa | grep "s349685"
L       s590861 +       s349685 -       0M      SR:i:8  L1:i:61 L2:i:16327

but, I cannot find the corresponding path in all 19 bed files that I generated.
(I used 'grep' command for find the path, but I got nothing)

I'm not sure how to interpret these results..!

Thanks,
Suyeon Wy