Analyses from X Chromosome Variation Paper

Daniel Cotter[1], Timothy Webster[2,3], Melissa Wilson[3,4]

2021

1. Department of Genetics, Stanford University
2. Department of Anthropology, University of Utah
3. School of Life Sciences, Arizona State University
4. Center for Evolution and Medicine, Biodesign Institute, Arizona State University

Analysis Steps

Step 1: Install/Set-up

Clone this repository and make sure conda is installed. Then use the provided PAB_variation.yml environment file to set up a new conda environment.

conda env create -f environment.yml

Step 2: Get data

Data should be downloaded from the provided links and copied into the data/ directory of the project folder.

Variant Data

Variant data is from The 1000 Genomes Project phase3 VCF files for chrX, chrY, & chr8:

• chrX: ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.vcf.gz

• chrY: ALL.chrY.phase3_integrated_v2a.20130502.genotypes.vcf.gz

• chr8: ALL.chr8.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

Genome masks

The strict mask as provided by The 1000 genomes Project is used for identifying monomorphic sites. It is provided as a whole genome bed file:

• Strict Mask: 20141020.strict_mask.whole_genome.bed

Population Lists

Population and subpopulation lists are calculated using:

• Population Panel: integrated_call_samples_v3.20130502.ALL.panel

We analyze all individuals across the X chromosome and chromosome 8 and we analyze all males across the Y chromosome. The option to analyze males or females for chrX and chr8 can be changed at the top by altering the global variable, SEX. Below, we have included the breakdown of the number of males and females in each population:

AFR Populations	AMR Populations	EAS Populations	EUR Populations	SAS Populations
POP Females Males ACB 49 47 YRI 56 52 ASW 35 26 ESN 46 53 MSL 43 42 GWD 58 55 LWK 55 44 TOTAL 342 319	POP Females Males MXL 32 32 PUR 50 54 CLM 51 43 PEL 44 41 TOTAL 177 170	POP Females Males CHB 57 46 JPT 48 56 CHS 53 52 CDX 49 44 KHV 53 46 TOTAL 260 244	POP Females Males CEU 50 49 TSI 54 53 FIN 61 38 GBR 45 46 IBS 53 54 TOTAL 263 240	POP Females Males GIH 47 56 PJL 48 48 BEB 44 42 STU 47 55 ITU 43 59 TOTAL 229 260

Population codes can be found here.

Step 3: Run the analysis

Run the analysis using snakemake once all of the raw data files are downloaded. Navigate to the top of the project directory and type the following commands:

conda activate chrX_variation
snakemake

An example of this process for the YRI population is presented below:

This workflow contains 34 jobs while the workflow for all of the figures in the paper contains 1,737 jobs.