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Is gaf.gz supported by vg pack and gamsort?
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Does vg giraffe output secondary and supplimentary alignments?
written by lushjia 0I'm using `vg giraffe` to align short-read sequencing data to a minigraph-cactus pangenome graph. When I checked some repetitive regions, I noticed that reads that …
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How to generate a GAF that shows alignments to all component genomes in graph
written by peterdfields 4I'm trying to generate a GAF (with reference rather than node coordinates) which describes how an individual long-read maps to all the different components of …
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Vg Call error multiple paths detected using HPRC-GRCH38 ref
written by Alexandria A. 0Hi vg team, I am attempting to use vg call on a wgs sample aligned to hprc-grch38, using wdl Cromwell. I'm pretty new to cs …
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VG : No reference-sense paths available in the graph; falling back to generic paths.
written by Hang 1Hi, I was aligning short reads to a customized gfa file using vg giraffe. I tried to extract mapped reads from the gam files, first …
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why does vg convert doesn't work?
written by Michal 0I am using vg version 1.49.0 on Ubuntu I am trying to convert a gam file to a gfa format and it is not working. …
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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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Vg gamsort temporary folder
written by arunkumarramrsh 4Hi, I was trying to use vg gamsort to sort and index the gam file so as to use vg chunk later. I get the …
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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 …