User: glenn.hickey

gravatar for glenn.hickey
glenn.hickey160
Reputation:
160
Status:
Trusted
Location:
Last seen:
9 hours ago
Joined:
10 months, 4 weeks ago
Email:
g***********@gmail.com

Posts by glenn.hickey

<prev • 23 results • page 1 of 3 • next >
0
votes
1
answer
115
views
1
answers
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 11 days ago by glenn.hickey160
1
vote
2
answers
183
views
2
answers
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.hickey160 • updated 8 weeks ago by RamRS30k
0
votes
2
answers
183
views
2
answers
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.hickey160
0
votes
1
answer
203
views
1
answers
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.hickey160
1
vote
1
answer
170
views
1
answers
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 3 months ago by glenn.hickey160
0
votes
2
answers
130
views
2
answers
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 3 months ago by glenn.hickey160
0
votes
1
answer
112
views
1
answers
Answer: A: How can i use several samples of resequencing data to get a visualize paths
... 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.hickey160
1
vote
1
answer
162
views
1
answers
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.hickey160
1
vote
1
answer
176
views
1
answers
Answer: A: vg map with long assembled contigs
... 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.hickey160
1
vote
1
answer
172
views
1
answers
Comment: A: passing a third-party GFA to vg tools
... 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.hickey160

Latest awards to glenn.hickey

Scholar 11 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 3 months ago, created an answer that has been accepted. For A: Merging .gam files

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1497 users visited in the last hour