Is there support for translation between stable coordinate and segment/local coordinate for GAF?

[SHuang-Broad]

Hello Heng,

I'm getting myself familiar with the GAF format.
One site of interest to me (an INS onto GRCh38), has several reads with the following column 6 (broken down for easier viewing):

>CHM13#0#chr18:67654357-67665821
<HG02145#2#h2tg000315l:763450-763480
>CHM13#0#chr18:67666067-67666203
>HG00735#1#h1tg000016l:20472026-20472231
>CHM13#0#chr18:67666258-67666722
<HG00621#2#h2tg000001l:12875529-12875687
>CHM13#0#chr18:67666724-67672585
>chr18:67453985-67471633

which translates, by hand (I did it, so there might be errors) to the segment coordinate

>s132736>s132737>s132738>s132739<s204376>s132742>s164264>s164265>s132745>s132746>s132747>s132748<s150020>s132750>s132751>chr18:67453985-67471633

I know that minigraph can output GAF in the second format via --vc.

I am wondering if there's any tool in gfatools that does this translation between the two coordinate systems? This way a sound round of mapping can be avoided.

Thanks!
Steve

[lh3]

Sorry for the late response. mgutils.js in minigraph/misc can translate "--vc" output to stable output. However, there are no tools to do the opposite.