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User: glenn.hickey

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glenn.hickey • 220
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Posts by glenn.hickey

<prev • 27 results • page 1 of 3 • next >
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Answer: A: Handling of Reverse Strand in GAM file
... There is some documentation on the GAM format here: https://github.com/vgteam/libvgio/blob/master/deps/vg.proto Note that in vg we are phasing out GAM in favour of GAF: https://github.com/lh3/gfatools/blob/master/doc/rGFA.md#the-graph-alignment-format-gaf with "cs" cigar tags as defined here: https ...
written 19 days ago by glenn.hickey • 220
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Answer: A: empty vcf from vg call
... The commands look okay (though `vg snarls` seems to be missing). Assuming your snarls file is fine, the other reason for an empty VCF could be not enough mappings found in the pack file. You can use `vg depth -k -b 10000` to verify the coverage in your pack file (and with `-g` to verify the covera ...
written 19 days ago by glenn.hickey • 220
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Answer: A: Issue on vg call order of paths
... Your assumption is correct: `vg call` finds all paths through a bubble (subsetting to those specified with -p), and chooses the first from an alphabetical sorting. There is no interface to change this, presently. I'd be curious to know what exactly your use case is and why you want this functiona ...
written 19 days ago by glenn.hickey • 220
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Answer: A: vg call has very different variant number between xg and hg
... It is important that the same graph be used for both the `pack` and `call` commands. In your xg example, you are packing with the `xg` and calling with the `vg`. This will produce undefined results. If you pack and call with the same graph, the output should be identical regardless of the format. ...
written 19 days ago by glenn.hickey • 220
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Answer: A: Whole genome alignment graph building
... Another method in development is https://github.com/pangenome/pggb We are also making some changes to cactus to make it easier and more practical to use for pangenomes (as opposed to interspecies alignments) -- look out for them in a release soon. ...
written 3 months ago by glenn.hickey • 220
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Answer: A: Merge multiple vcfs vgtools
... The `-a` option can now be used with `vg call` to add reference calls: https://github.com/vgteam/vg/pull/2966 vg call -a ... -s sample1 > sample1.vcf vg call -a ... -s sample2 > sample2.vcf etc. Then `bcftools merge sample1.vcf.gz sample2.vcf.gz -m all` to make the combined VCF. ...
written 5 months ago by glenn.hickey • 220 • updated 5 months ago by _r_am ♦ 32k
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Answer: A: Merge multiple vcfs vgtools
... This only works right now in "genotyping mode", where you construct a graph from a VCF with `vg construct -a` then genotype that same VCF with `vg call -v`. I'm hoping to have a solution for general graphs, in the form of an option that makes `vg call` call every site with consistent positions no ...
written 5 months ago by glenn.hickey • 220
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Comment: C: GAF format from vg
... Yes, it is the GAF as defined on that page that vg outputs. Note that it currently writes the `` (as opposed to ``) coordinates. ...
written 5 months ago by glenn.hickey • 220
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Answer: A: Vg call in a specific region
... It's less necessary to break the graph into tiny chunks with `vg chunk -p`. Here's an example on chunking by chromosome: https://github.com/vgteam/vg/wiki/Whole-genome-calling-and-genoyping#calling-the-graph-by-first-splitting-into-components That said, workflows like that should still work. Yo ...
written 6 months ago by glenn.hickey • 220
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Answer: A: vg deconstruct with path sizes
... If I understand correctly, you want the length of each allele stored in some kind of VCF Format field? I suppose this is possible, but as far as I know, must VCF parsers would be parsing the alleles into strings in memory anyway which would allow you to get the size just as efficiently. As mentio ...
written 6 months ago by glenn.hickey • 220

Latest awards to glenn.hickey

Scholar 19 days ago, created an answer that has been accepted. For A: Merging .gam files
Scholar 3 months ago, created an answer that has been accepted. For A: Merging .gam files
Scholar 6 months ago, created an answer that has been accepted. For A: Merging .gam files
Scholar 7 months ago, created an answer that has been accepted. For A: Merging .gam files
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