Summary statistics munggling

[gaow]

I would like to revisit the issue of summary statistics munggling. This will be a preprocessing step to pecotmr.

I would like to provide tutorials / recipes / pipelines based on work from our Sinai colleagues, https://github.com/neurogenomics/MungeSumstats

Unfortunately this is not what's done in xqtl-pipeline -- because at that time the person I delegate to implement this feature ignored my suggestion and wrote something on his own.

Later Hao compared the differences:

StatFunGen/xqtl-protocol#212

We don't have to reinvent the wheels (again!) in pecotmr. We just need a good vignette on preprocessing and basic QC using MungeSumstats?

[gaow]

MungeSumstats supports standardizing variants to given genomic builds. In FunGen-xQTL we preprocess the data to align to a very specific reference genome file, see [qc_1] of https://cumc.github.io/xqtl-pipeline/code/data_preprocessing/genotype/VCF_QC.html# bcftools norm.

I don't know if MungeSumstats would do the same, or we would better build a reference genome package from our fasta file just in case : https://www.bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf