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conversion of GFA to rGFA
@lh3, I'm curious to know , whether we can convert GFA
to rGFA
? . As per rGFA format, we need to maintain 3 additional information along with each segment lines (S
). So,
Assuming we have GFA
with segments links;
S s1 AAT
S s2 T
can't we just add ;
S s1 AAT LN:i:3 SN:Z:chr1 SO:i:90374744 SR:i:0
S s2 T LN:i:1 SN:Z:chr1 SO:i:176753158 SR:i:0
Will it be valid rGFA
?
A GFA to rGFA tool would be extremely helpful for my use case at the moment. At a minimum, I could use more information about how the SO value is calculated; it's not 100% clear to me, and trying to determine what it should be while parsing the reference human pangenome freeze 1 (which only has intermittent SO tags) has proven to be unexpectedly complex!
I think the reverse is true, a rGFA to GFA
conversion tool is (also) severely lacking.
While minigraph is apparently the most efficient and promising pangenome tool at present, the use of rGFA prohibits downstream analysis using the odgi and vg toolkits (at least to my knowledge). Therefore, no SNP calling, odgi pavs calling etc is possible.