Erik Garrison
Sorry, then the output will go directly to BAM. Otherwise, to convert the GAM, use vg surject. On Thu, Jul 30, 2020 at 12:56 PM Erik Garrison wrote: > You...
We have not been able to use VG deconstruct for many versions now. It doesn't parse the pggb pan-sn naming correctly. There has been a regression. The version installed by...
@glennhickey https://github.com/pangenome/pggb/blob/master/pggb#L620-L621 ```bash echo "[vg::deconstruct] making VCF with reference=$ref and delim=$delim" ( TEMPDIR=$(pwd) $timer -f "$fmt" vg deconstruct -P "$ref" \ -H "$delim" -e -a -t $threads "$prefix_smoothed_output".final.gfa >"$vcf" )...
We're stuck on v1.40.0: https://github.com/pangenome/pggb/blob/master/Dockerfile#L97 ``` wget https://github.com/vgteam/vg/releases/download/v1.40.0/vg ... ```
@glennhickey sure http://hypervolu.me/~erik/yeast/cerevisiae.fa.gz.d1a145e.417fcdf.7493449.smooth.final.gfa.gz
Any update on this?
If you want to model multiallelic and complex nested variation, you can build a variation graph and apply the GBWT. This implicitly generalizes the PBWT to multiallelic states. But you...
Would it make sense to just change the hash functions used in the construction of the pmhf? If these tend to be locality sensitive then this would tend to drive...
A metric to optimize would be the edit distance between a query and the kmer it is hashed to "flasely". We want to be more likely to hash to *something*...
Could I just put this kind of l-minimizer hash in as the custom hash function? What else might I need to adjust?