User: glenn.hickey

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glenn.hickey170
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Posts by glenn.hickey

<prev • 23 results • page 2 of 3 • next >
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Answer: A: Merging .gam files
... GAM files can be combined with `cat`. Note that `vg call` can only genotype one sample at a time, though. ...
written 5 months ago by glenn.hickey170
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Answer: A: vg sv calling
... No, unfortunately not. Nodes and edges in vg's graph model correspond to exact positions. In theory, you can store every possible deletion that you see in your data within one graph. But in practice, there is a point of diminishing returns when adding too much similar variation to a graph, and it ...
written 8 months ago by glenn.hickey170
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Answer: A: vg docker image
... A docker image is published for each release. You can see the releases here: https://github.com/vgteam/vg/releases. The docker image is 3 lines below the big green download button. ...
written 8 months ago by glenn.hickey170
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Answer: A: How do I deal with duplicate reads when using vg to analyse WGS data?
... This is a great question. There is indeed no vg tool yet to mark duplicates. The only workaround, which isn't great, is to use a BAM file to detect duplicates. Please make a feature request on github! We are working on some changes to replace GAM as a default format which should make it possibl ...
written 9 months ago by glenn.hickey170
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Answer: A: Segmentation fault (core dumped) during vg surject
... The commands look okay, so this could be a bug. If you are able to share your data, please raise an issue on Github https://github.com/vgteam/vg/issues/new?assignees=&labels=&template=report-a-bug.md&title= and we' should be able to fix it. Other things to try: the very latest vg rele ...
written 9 months ago by glenn.hickey170
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Answer: A: Edit distance of an alignment
... You are probably best to use the "score" field, as "identity" doesn't take into account gaps. The default scoring parameters are displayed under the "scoring:" section if you run vg map without any arguments. With the defaults, a perfect score is 10 + length of the read. ...
written 9 months ago by glenn.hickey170
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Answer: A: More haplotype threads than expected
... Ambiguities, conflicts or missing data in the phasing information in the VCF will cause the haplotype threads to be broken up. Adding the `-P` option to your `index -G` command to force phasing at unphased genotypes may resolve this. ...
written 10 months ago by glenn.hickey170
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Answer: A: Extracting specific regions(ex, chr1:100-200 of hg38) from whole genome .vg and
... You can extract regions from a GAM with `vg chunk` but it's clunky. Index the GAM (very slow): vg gamsort aln.gam -i aln.sorted.gam.gai > aln.sorted.gam Extract the chunk: vg chunk -x graph.vg -a aln.sorted.gam -g -p chr1:100-200 -c 10 > chunk.vg The `-c 10` specifies how far f ...
written 10 months ago by glenn.hickey170 • updated 10 months ago by h.mon31k
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Answer: A: How to determine haplotypes from variation graphs
... This is a problem we're interested in, but there's nothing yet built into vg for doing this. I believe the whatshap devlopers (https://bitbucket.org/whatshap/whatshap/src/master/) have been working on vg support, but I do not know what state it's in currently. ...
written 10 months ago by glenn.hickey170
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Answer: A: VG view command hangs with no result (VG Toolkit)
... The `.vg` format is very inefficient. Loading a whole-genome .vg file is both slow and very memory-intensive. We have replacement formats that are much better and are working to (transparently) integrate them throughout the vg toolchain, including GFA conversion. In the meantime, your safest bet ...
written 10 months ago by glenn.hickey170

Latest awards to glenn.hickey

Scholar 7 weeks ago, created an answer that has been accepted. For A: Merging .gam files
Scholar 4 months ago, created an answer that has been accepted. For A: Merging .gam files
Scholar 5 months ago, created an answer that has been accepted. For A: Merging .gam files

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