User: glenn.hickey
glenn.hickey • 160
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Posts by glenn.hickey
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... 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 11 days ago by
glenn.hickey • 160
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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 8 weeks ago by
glenn.hickey • 160
• updated
8 weeks ago by
RamRS ♦ 30k
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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 9 weeks ago by
glenn.hickey • 160
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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 10 weeks ago by
glenn.hickey • 160
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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 3 months ago by
glenn.hickey • 160
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... 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 3 months ago by
glenn.hickey • 160
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... You can make the dot output a bit smaller by passing `-S` to `vg view`. You can also subset to a region of interest with `vg find -p chr1:500-600 | vg view - pd ...`. Or you can try the interactive viewer here https://github.com/vgteam/sequenceTubeMap.
...
written 3 months ago by
glenn.hickey • 160
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Answer:
A: Converting gam to gaf
... 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` ...
written 3 months ago by
glenn.hickey • 160
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... Some alternatives to vg map for long reads are
- vg mpmap -S --read-length long
- GraphAligner: https://github.com/maickrau/GraphAligner
...
written 3 months ago by
glenn.hickey • 160
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... It's something we're working on. I think the main issue is that we only support numeric node ids in vg. ...
written 3 months ago by
glenn.hickey • 160
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