Peter VandeHaar

Now that it's implemented, can you close this PR?

Yeah, the branch https://github.com/statgen/pheweb/tree/neglog10 tries to switch over from storing pvalue to neglog10pvalue but I haven’t finished it yet. Is that something you’re interested in helping with?

### TODO: - [ ] Allow `HWE_LPVAL` and `HWE_LLR` to drift by 1% in `test/indel/expected/indel/final/all.genotypes.vcf.gz` and `test/indel/expected/indel/final/merge/all.genotypes.20.bcf`. - screenshot in https://github.com/statgen/gotcloud/commit/c546acd1c23933e24db4c62c0c6e56bd87cf228a#commitcomment-21688567 - Make sure that people think this change is...

What command are you running?

### TODO: - [ ] add `cmake g++ libz-dev libncurses5-dev` to `check_requirements.sh` - [ ] allow any ssl ≥`0.9.8` (and deal with fallout later) - [ ] check for either...

Thanks for pointing this out and finding the relevant parts of the documentation. I believe that you are correct. bamUtil won't warn if the CIGAR is `*`, but doesn't check...

Do you think that clipOverlap clipped some reads that should not have been clipped? Can you find any reads that overlap that position that were clipped? Do you see whether...

In the code you ran in issue https://github.com/statgen/bamUtil/issues/16, were some quality scores changed? Could that be the cause? Are your unmodified bams from before that code, or after it? (Again,...

Back to [mktrost's question from earlier](https://github.com/statgen/bamUtil/issues/20#issuecomment-171448459): When you look at the reads supporting the missing variant (and maybe their mates)– are there any differences (other than the CIGAR changes that...

There's two ways to deal with the single-threaded time taken by `pheweb matrix`: (a) Parallelize `pheweb matrix`. (b) Instead of running `pheweb process`, run ``` pheweb phenolist verify && pheweb...