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Is gaf.gz supported by vg pack and gamsort?
written by gulin 1I am inspired by the article: https://jmonlong.github.io/manu-vggafannot/. I am not working well with gam format. So I am thinking about build a pipline based on …
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mismatch sites from GAM/GAF
written by zhengluo 0I would like to know if mismatch sites can be extracted directly from GAM/GAF files.
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Does vg stats support gaf file?
written by Wang Cong 2Hi, I am trying to get alignment stats from a gaf file using vg stats -a <gaf> and got a long error. May I ask …
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Gam format specification
written by guntul 4Hi everyone, I am dealing with gam file format and trying to understand its structure. I convert my gam files to JSON using vg. I …
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Can a read be aligned more than once?
written by guntul 4In linear reference(sam,bam) or in pangenomic alignment(gam,gaf), is it possible to a read that is aligned twice or more? Can we observe that a read …
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Key-value pairs at the end of lines of gaf/paf files
written by guntul 4Hi everyone, I dont understand what the optional strings at the end lines of paf and gaf files really mean? [This link][1] and [this link][2] …
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Difference between gam and sam/bam files?
written by Uveyik 8Hi everyone, I am trying to understand pangenomic data/file formats. In the vg's descripton of file format, it says gam is similar to sam/bam and …
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vg convert does not preserve the order of the reads
written by Yihang 0When I use `vg convert` (v.1.39) to convert a `gam` file to a `gaf` file (or vice versa), I find that the order of the …
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Retrieving alignment scores with vg surject
written by Gabriela 0Hello! I'm trying to get multiple alignments with their corresponding **alignment scores** for paired-end reads against a pangenome using `vg giraffe`, and then `vg surject` …
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Converting gam to gaf
written by hmg 2I noticed it is now possible to output alignments in gaf files instead of gam, which is great! How difficult would it be to convert …