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Converting gam to gaf
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14 months ago
hmg ▴ 20

I noticed it is now possible to output alignments in gaf files instead of gam, which is great! How difficult would it be to convert gam to gaf? Gaf is definitely easier to parse than using jq for the json conversion of gam, but I'd like to avoid realigning all my previous work. Are there plans to make a gaf output option for vg view?

vg • 361 views
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Entering edit mode
13 months ago
glenn.hickey ▴ 240

GAF will gradually be more tightly integrated with all the tools. In the meantime, you can convert back and forth between GAM and GAF with vg convert -F and -G

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