vgraph

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Hope it helps.

erikbgithub

Citation

1

Is there an available manuscript which describes this tool? I've seen this work cited in recent publications, but only this repository is cited. I ask because I'd like to develop...

ghost

Hello, I'm amazed how well `vgraph` works. What I would really like to have, is a way to see, why there is a mismatch between two samples. This can be...

finswimmer

Support for .vg and other graphical genome data formats

1

I'd like to use vgraph to compare different "variation" graphs, in the [vg](https://github.com/vgteam/vg) sense. Could vgraph or its algorithms be applied to the DAG-like parts of generic genome graphs?

ekg

help interpreting output

7

Hi Kevin, I was looking at some GIAB data this morning and found the link to your tool. I gave it a whirl with this command: `vgraph repmatch --include-regions GIAB/HG001_GRCh37_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel.bed...

RichardCorbett

A fresh install of vgraph on a clean linux system gives the following error: > root@5dda7d88618a:/data#` vgraph > Traceback (most recent call last): > File "/usr/local/bin/vgraph", line 9, in >...

mendezg

Does vgraph compare gVCFs of various forms? Aside from the standard form on page 24 of gVCF [spec](https://samtools.github.io/hts-specs/VCFv4.3.pdf) where a symbolic alt allele indicates a hom ref block, GATK uses...

lijiayong

Might be nice to have support for VCFs read though URLs instead of files. That way we could annotate against VCFs stored in remote DBs more easily.

brendanofallon

In some cases it's handy to be able to compare VCFs without sample information - for instance, to see which variants in some query VCF match those in, say, the...

brendanofallon

Cleaning up setup script to make it more universal

5

Hi Kevin, Thanks so much for creating this tool! I made a few trivial changes that makes the setup more universal (hopefully) and lets it work on my mac, for...

ghost