User: xwwang

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xwwang20
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20
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New User
Location:
Gerogia , USA
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Last seen:
6 days, 23 hours ago
Joined:
3 months ago
Email:
x*****@uga.edu

Posts by xwwang

<prev • 9 results • page 1 of 1 • next >
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Issue on vg call order of paths
... The genome graph is created from multiple genome alignment with 'vg construct', e.g. from 4 genomes, named: A, B, C, D Now we want to call variants with ‘vg call’ from packed graph alignment file (.pack). Command: vg call -t 10 graph.vg -k graph.pack -a >graph.gam.vcf [This will use defa ...
vg written 21 days ago by xwwang20 • updated 15 days ago by glenn.hickey220
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vg call has very different variant number between xg and hg
... I find that the `vg call` has a very different number of variants between calling from the xg, xg packed file and hg (hashgraph), hg packed file. How to explain this? Which one is recommended? command: tested vg version 1.27, 1.29 ## For xg mode: vg pack -x $graph.xg -g $graph.gam -t 10 - ...
vg written 4 weeks ago by xwwang20 • updated 15 days ago by glenn.hickey220
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how to view .gam near to given node IDs or path positions
... It is interesting to view the alignment in .gam from vg map output. The basic visualization of vg wiki site has demostrated to show the alignment in .gam of a whole graph. However, there is no information to show how to view a .gam at interesting node site(s), or position of a path, meaning just vi ...
vg written 4 weeks ago by xwwang20
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how to call variance from vg multiple path alignment "mpmap" .gamp
... Is there any instruction on how to call variance from vg's multiple path map output? I did not find information on how to call variance from multiple path map output. details: #the multiple path map alignment output (.gamp) from mpmap and works well Command: vg mpmap -x $graph.xg -g $graph.gcsa - ...
vg written 6 weeks ago by xwwang20
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Answer: A: vg path associated with sample name
... Thanks a lot. It is much clear now. ...
written 10 weeks ago by xwwang20
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vg path associated with sample name
... Is there any way to associate the pathname in vg graph with sample ID? details: the vg graph is generated from variants in vcf of multiple samples How to know each path of vg graph is associated or tagged with variant source tag, e.g. sample ID? Thanks. ...
vg written 12 weeks ago by xwwang20
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vg gam file statistics: how many reads are mapped
... Is there any existing tool which can calculate how many reads are mapped in .gam file which is generated by command: vg map for example the .gam file is "graph.read.gam" ...
vg written 12 weeks ago by xwwang20 • updated 10 weeks ago by Jouni Sirén130
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Answer: A: vg paired end short read mapping: Best practice?
... In my experience, you can use the multiple threads to speed up via the -t option: -t $nthread where $nthread is the number of threads, e.g. 10 In this way, it will be much fast. It took me one day for 200 million paired-end reads to map to a large graph. ...
written 3 months ago by xwwang20
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vg mapping comparison: graph vs flat graph
... Is there any way to do a vg mapping comparison: Two vg gam files: 1. one from the flat graph constructed from a ref genome only 2. another graph constructed from a ref genome and variants after mapping, the same set of reads were mapped to either graph with "vg map", I would like to see how muc ...
mapping improvement vg written 3 months ago by xwwang20

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