LocalAncestry

Roshni Patel ([email protected])

Description

Calling local ancestry tracts with RFMix v1.5.4 and (optionally) validating global ancestry fractions with ADMIXTURE.

NCBI build

This pipeline was designed to call local ancestry tracts on hg38 VCFs. In practice, it can be used to call local ancestry tracts on hg19/GRCh37 VCFs, but you will need to obtain hg19/GRCh37 versions of the files in maps/. hg19/GRCh37 genetic maps in the same format can be found here. chrom_centromere.map will probably have to be recreated manually starting from the file centromeres_hg19.bed here.

Cluster

This pipeline is designed to be run on a cluster that uses the Slurm workload manager. If this is not the case, sm_script.sh and sm_slurm_config.json will need to be reworked.

Required files

See scripts/snakemake_variables.py for more details on naming conventions and directory structure.

Programs

• RFMix v1.5.4
• ADMIXTURE (optional)

Data

• Phased VCF containing admixed data
• Phased VCF containing reference data
• Metadata file for admixed individuals (mapping ancestry to VCF sample ID)
• Metadata file for reference population (mapping ancestry to VCF sample ID)

Workflow

1. Obtain required files
2. Determine whether your admixed and reference VCFs have the same chromosome naming system; otherwise you might want to uncomment rule annotate_admix in the Snakefile and modify accordingly to suit your purposes.
3. Edit variables in scripts/snakemake_variables.py as needed. (In all likelihood, only the variables under Data and Programs will need to be edited.)
4. Edit sm_slurm_config.json with the partitions you'll be running jobs on.
5. Edit the top of sm_script.sh and the top of the Snakefile to reflect the location/type of shell you're using.
6. Determine desired output and edit rule all in Snakefile as needed.

• To generate local ancestry tracts with RFMix:

rule all:
    input:
        expand(DATA_DIR + "bed/em{em}.chr{chr}.{ind}.{hapl}.bed", hapl=HAPL, ind=INDIV, em=EM_ITER, chr=CHROMS)

• To plot karyograms with RFMix local ancestry tracts:

rule all:
    input:
        expand("plots/{ind}.em{em}.png", ind=INDIV, em=EM_ITER)

• To generate per-chromosome global ancestry fractions from RFMix:

rule all:
    input:
        expand(DATA_DIR + "chr{chr}/chr{chr}.em{em}.lai_global.txt", chr=CHROMS, ind=INDIV)

• To generate genome-wide global ancestry fractions from both RFMix and ADMIXTURE:

rule all:
    input:
        DATA_DIR + "combined_global_anc_frac.txt"

• (Note: there is currently no way to generate genome-wide global ancestry fractions for RFMix alone, but you can edit scripts/combine_chrs.py to allow for that.

7. Make the conda environments in envs/
8. Unzip maps/plink.GRCh38.genetic_map.zip
9. Run the pipeline with ./sm_script.sh