gfatools view to subset a gfa file

[Dkyuan]

Hi, sir:

I wanted to subset a gfa file from a region (eg: Chr01:1-10000) , and I thought the parameter -R might help, but got a empty file, may your help me with the right code: The code I used:

[path to]/gfa view -R Chr01:1-10000  -r 1 my.gfa >1_10k.gfa
 # I tried -r 1 , -r 10, or without -r
# I also tried -l Chr01:1-10000 with or without -r parameter

It output a empty file 1_10k.gfa

I used vg to construct the graph genome .vg, then got the gfa file.

the example code was successful:

./gfatools view -l MTh4502 -r 1 test/MT.gfa >test/sub.gfa

Thanks for your time.

[pioneer-pi]

I am also confused about -R option, each time I use it, I will get an empty file. However, -l is useful. When I use ./gfatools view -l 1,2,3 my.gfa > subgraph.gfa, the result is segment 1,2,3 and related segments and links.

[Dkyuan]

@pioneer-pi

Thanks for sharing. Yes, -l is useful as the example.

I use vg find to get a subset gfa file now: vg find -x your.xg -p your_region -c 3 |vg view - > out.gfa