QTL analysis using European only data¶

In this notebook I document procedures analyzing eQTL and sQTL with MASH, using European only data from GTEx.

Input data¶

Summary statistics for EUR only eQTL and sQTL, from fastqtl analysis.

Data format conversion for MASH input¶

First I obtain a list of available genes and available summary stats data,

[global]
from glob import glob
parameter: ss_dir = path('/project2/mstephens/gaow/gtex_v8_eqtl_eur_only')
parameter: out_dir = path(f"{str(ss_dir).rstrip('/')}_output")
data_files = glob(f'{ss_dir:a}/*')

[get_meta_1]
with open(f"{out_dir:a}/{ss_dir:b}.sumstats_list", 'w') as f:
    f.write('\n'.join(data_files))

[get_meta_2]
input: data_files, group_by = 1, concurrent = True
output: f"{out_dir:a}/{_input:bn}.genes_list"
task: trunk_workers = 1, trunk_size = 2, walltime = '1h', mem = '1G', cores = 1, tags = f'{_output:bn}'
bash: expand = True
    zcat {_input} | cut -f 1 | tail -n +2 | sort -u > {_output}
    
[get_meta_3]
# obtain a list of loci that shows up in all conditions
input: group_by = 'all'
output: f"{out_dir:a}/{ss_dir:b}.genes_list"
python: expand = "${ }"
    data = []
    for item in [${_input:r,}]:
        data.append([x.strip() for x in open(item).readlines()])
    data = sorted(list(set.intersection(*map(set,data))))
    with open(${_output:r}, 'w') as f:
        f.write('\n'.join(data))

sos run European_QTL.ipynb get_meta -c midway2.yml -q midway2 --ss-dir /project2/mstephens/gaow/gtex_v8_eqtl_eur_only
sos run European_QTL.ipynb get_meta -c midway2.yml -q midway2 --ss-dir /project2/mstephens/gaow/gtex_v8_sqtl_eur_only

Then I'm ready to run the data format conversion,

[convert]
parameter: cols = list
bash: expand = True
    sos run fastqtl_to_mash.ipynb \
        --cwd {out_dir:a}/fastqtl_to_mash_output \
        --data-list {out_dir:a}/{ss_dir:b}.sumstats_list \
        --gene-list {out_dir:a}/{ss_dir:b}.genes_list \
        -c midway2.yml -q midway2 --common-suffix ".txt" \
        --cols {paths(cols)}

sos run European_QTL.ipynb convert --ss-dir /project2/mstephens/gaow/gtex_v8_eqtl_eur_only --cols 8 9 7
sos run European_QTL.ipynb convert --ss-dir /project2/mstephens/gaow/gtex_v8_sqtl_eur_only --cols 7 8 6

Run MASH pipeline¶

[mash]
bash: expand = True
    sos run mashr_flashr_workflow.ipynb mash \
    --cwd {out_dir:a}/mashr_flashr_workflow_output \
    --data {out_dir:a}/fastqtl_to_mash_output/{ss_dir:b}.mash.rds \
    --vhat mle -c midway2.yml -q midway2

sos run European_QTL.ipynb mash --ss-dir /project2/mstephens/gaow/gtex_v8_eqtl_eur_only
sos run European_QTL.ipynb mash --ss-dir /project2/mstephens/gaow/gtex_v8_sqtl_eur_only