Peter VandeHaar

How many cores on the machine? `pheweb process -h` will show all the steps it runs. The only heavy one remaining is `pheweb gather-pvalues-for-each-gene`, which is 4x faster than `pheweb...

Yep, it's multithreaded.

@hanayik I'm not aware of such a fork. I'd love to have a parallel matrix feature and I can help if you'd like to work on it. Changes would be...

@Shicheng-Guo Yeah, if your system is CPU-limited (rather than IO-limited), then reducing the gzip compression level will probably make `pheweb bgzip-phenos` 2x-3x faster. Unfortunately, I don't think pysam lets you...

Do you mean that internally pheweb should store everything in tabixed bgzipped GWAS-VCF instead of the current tabixed bgzipped tsv files? Why? How would that make queries more efficient? Or...

**Use nitro, without `make`:** Chris pointed out that I should subvert the Makefile workflow and use a `.nitro` file. The commands must be taken from the `Makefile` to deal with...

This is a great bug report, thanks. Can you show me the line in your input file with `6,351611`? And also the line with `3516110.016`? `pos` is treated as an...

Approaches: - a file tabixed by rsid - if the rsid-only file is sorted by rsid, we could hold the last tabixed block in a cache (maybe even in a...

(replaces https://github.com/statgen/pheweb/issues/43)

[UCSC Track Search](https://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=637718941_VogxeiPOijJQZnFAldVRAdH3WYGO&hgt_=1508973590&db=hg19&tsCurTab=simpleTab&hgt_tsDelRow=&hgt_tsAddRow=&hgt_tsPage=&tsSimple=recombination&hgt_tSearch=search&tsName=&tsDescr=&tsGroup=Any&tsType=Any&hgt_mdbVar1=cell&hgt_mdbVal1=Any&hgt_mdbVar2=antibody&hgt_mdbVal2=Any) has some deCODE-based recombination rate built in 2010 for GRCh36/hg18 that are apparently lifted to GRCh37. Nothing on GRCh38. ([paper](http://www.nature.com/nature/journal/v467/n7319/abs/nature09525.html), [related webpage](http://hgsv.washington.edu/cgi-bin/hgTrackUi?hgsid=2699407_Ab3iwTB9PueS6FGgE4bZA7uT462j&c=chr7&g=decodeRmap))