Modules reviewed by @gaow

[gaow]

@hsun3163 this ticket keeps track of modules that I (re)reviewed : at this round I mostly make all the changes myself and try to finalize everything. Every time I finalize a module I'll post an update. Please be very careful not to make heavy changes on codes that I finalized without discussing with me first.

Finalized codes for V 1.0 release:

• GWAS QC
• PCA
• HG reference data preprocessing
• RNA calling
• Sample level RNA-seq QC
• genotype data formatting
• VCF QC
• Normalization
• Gene coord annotation

In progress by @gaow:

Pending 2nd round of test @hsun3163 -- both with MWE and with ROSMAP data

• [x] GRM LOCO
• [x] PEER -- works for Wenhao's MWE but need to use our MWE to connect to next steps
• [x] Bi-CV -- add your old MWE

[gaow]

List of improvements still needed (I'll keep on adding to it):

• [ ] In this folder https://www.synapse.org/#%21Synapse:syn36422500 remove the stderr files
• [ ] Since we require a header here, https://cumc.github.io/xqtl-pipeline/code/molecular_phenotypes/calling/RNA_calling.html#input we must check after loading it to see if hte header is one of ID, fq1 fq2, read_length etc. In case people forget to put the header.