broadinstitute/tensorqtl

tensorQTL

tensorQTL is a GPU-enabled QTL mapper, achieving ~200-300 fold faster cis- and trans-QTL mapping compared to CPU-based implementations.

If you use tensorQTL in your research, please cite the following paper: Taylor-Weiner, Aguet, et al., Genome Biol., 2019.

Empirical beta-approximated p-values are computed as described in Ongen et al., Bioinformatics, 2016.

Install

You can install tensorQTL using pip:

pip3 install tensorqtl

or directly from this repository:

$ git clone [email protected]:broadinstitute/tensorqtl.git
$ cd tensorqtl
# set up virtual environment and install
$ virtualenv venv
$ source venv/bin/activate
(venv)$ pip install -r install/requirements.txt .

To use PLINK 2 binary files (pgen/pvar/psam), pgenlib must be installed:

git clone [email protected]:chrchang/plink-ng.git
cd plink-ng/2.0/Python/
python3 setup.py build_ext
python3 setup.py install

Requirements

tensorQTL requires an environment configured with a GPU for optimal performance, but can also be run on a CPU. Instructions for setting up a virtual machine on Google Cloud Platform are provided here.

Input formats

Three inputs are required for QTL analyses with tensorQTL: genotypes, phenotypes, and covariates.

• Phenotypes must be provided in BED format, with a single header line starting with # and the first four columns corresponding to: chr, start, end, phenotype_id, with the remaining columns corresponding to samples (the identifiers must match those in the genotype input). The BED file should specify the center of the cis-window (usually the TSS), with start == end-1. A function for generating a BED template from a gene annotation in GTF format is available in pyqtl (io.gtf_to_tss_bed).

• Covariates can be provided as a tab-delimited text file (covariates x samples) or dataframe (samples x covariates), with row and column headers.

• Genotypes must be in PLINK format, which can be generated from a VCF as follows:

  plink2 --make-bed \
      --output-chr chrM \
      --vcf ${plink_prefix_path}.vcf.gz \
      --out ${plink_prefix_path}
  

  If using PLINK 1.9 or earlier, add the --keep-allele-order flag.

  Alternatively, the genotypes can be provided as a dataframe (genotypes x samples).

The examples notebook below contains examples of all input files. The input formats for phenotypes and covariates are identical to those used by FastQTL.

Examples

For examples illustrating cis- and trans-QTL mapping, please see tensorqtl_examples.ipynb.

Running tensorQTL

This section describes how to run the different modes of tensorQTL, both from the command line and within Python. For a full list of options, run

python3 -m tensorqtl --help

Loading input files

This section is only relevant when running tensorQTL in Python. The following imports are required:

import pandas as pd
import tensorqtl
from tensorqtl import genotypeio, cis, trans

Phenotypes and covariates can be loaded as follows:

phenotype_df, phenotype_pos_df = tensorqtl.read_phenotype_bed(phenotype_bed_file)
covariates_df = pd.read_csv(covariates_file, sep='\t', index_col=0).T  # samples x covariates

Genotypes can be loaded as follows, where plink_prefix_path is the path to the VCF in PLINK format (excluding .bed/.bim/.fam extensions):

pr = genotypeio.PlinkReader(plink_prefix_path)
# load genotypes and variants into data frames
genotype_df = pr.load_genotypes()
variant_df = pr.bim.set_index('snp')[['chrom', 'pos']]

To save memory when using genotypes for a subset of samples, a subset of samples can be loaded (this is not strictly necessary, since tensorQTL will select the relevant samples from genotype_df otherwise):

pr = genotypeio.PlinkReader(plink_prefix_path, select_samples=phenotype_df.columns)

cis-QTL mapping: permutations

This is the main mode for cis-QTL mapping. It generates phenotype-level summary statistics with empirical p-values, enabling calculation of genome-wide FDR. In Python:

cis_df = cis.map_cis(genotype_df, variant_df, phenotype_df, phenotype_pos_df, covariates_df)
tensorqtl.calculate_qvalues(cis_df, qvalue_lambda=0.85)

Shell command:

python3 -m tensorqtl ${plink_prefix_path} ${expression_bed} ${prefix} \
    --covariates ${covariates_file} \
    --mode cis

${prefix} specifies the output file name.

cis-QTL mapping: summary statistics for all variant-phenotype pairs

In Python:

cis.map_nominal(genotype_df, variant_df, phenotype_df, phenotype_pos_df,
                prefix, covariates_df, output_dir='.')

Shell command:

python3 -m tensorqtl ${plink_prefix_path} ${expression_bed} ${prefix} \
    --covariates ${covariates_file} \
    --mode cis_nominal

The results are written to a parquet file for each chromosome. These files can be read using pandas:

df = pd.read_parquet(file_name)

cis-QTL mapping: conditionally independent QTLs

This mode maps conditionally independent cis-QTLs using the stepwise regression procedure described in GTEx Consortium, 2017. The output from the permutation step (see map_cis above) is required. In Python:

indep_df = cis.map_independent(genotype_df, variant_df, cis_df,
                               phenotype_df, phenotype_pos_df, covariates_df)

Shell command:

python3 -m tensorqtl ${plink_prefix_path} ${expression_bed} ${prefix} \
    --covariates ${covariates_file} \
    --cis_output ${prefix}.cis_qtl.txt.gz \
    --mode cis_independent

cis-QTL mapping: interactions

Instead of mapping the standard linear model (p ~ g), this mode includes an interaction term (p ~ g + i + gi) and returns full summary statistics for the model. The interaction term is a tab-delimited text file or pd.Series mapping sample ID to interaction value. With the run_eigenmt=True option, eigenMT-adjusted p-values are computed. In Python:

cis.map_nominal(genotype_df, variant_df, phenotype_df, phenotype_pos_df, prefix,
                covariates_df=covariates_df,
                interaction_s=interaction_s, maf_threshold_interaction=0.05,
                run_eigenmt=True, output_dir='.', write_top=True, write_stats=True)

The input options write_top and write_stats control whether the top association per phenotype and full summary statistics, respectively, are written to file.

Shell command:

python3 -m tensorqtl ${plink_prefix_path} ${expression_bed} ${prefix} \
    --covariates ${covariates_file} \
    --interaction ${interactions_file} \
    --best_only \
    --mode cis_nominal

The option --best_only disables output of full summary statistics.

Full summary statistics are saved as parquet files for each chromosome, in ${output_dir}/${prefix}.cis_qtl_pairs.${chr}.parquet, and the top association for each phenotype is saved to ${output_dir}/${prefix}.cis_qtl_top_assoc.txt.gz. In these files, the columns b_g, b_g_se, pval_g are the effect size, standard error, and p-value of g in the model, with matching columns for i and gi. In the *.cis_qtl_top_assoc.txt.gz file, tests_emt is the effective number of independent variants in the cis-window estimated with eigenMT, i.e., based on the eigenvalue decomposition of the regularized genotype correlation matrix (Davis et al., AJHG, 2016). pval_emt = pval_gi * tests_emt, and pval_adj_bh are the Benjamini-Hochberg adjusted p-values corresponding to pval_emt.

trans-QTL mapping

This mode computes nominal associations between all phenotypes and genotypes. tensorQTL generates sparse output by default (associations with p-value < 1e-5). cis-associations are filtered out. The output is in parquet format, with four columns: phenotype_id, variant_id, pval, maf. In Python:

trans_df = trans.map_trans(genotype_df, phenotype_df, covariates_df,
                           return_sparse=True, pval_threshold=1e-5, maf_threshold=0.05,
                           batch_size=20000)
# remove cis-associations
trans_df = trans.filter_cis(trans_df, phenotype_pos_df.T.to_dict(), variant_df, window=5000000)

Shell command:

python3 -m tensorqtl ${plink_prefix_path} ${expression_bed} ${prefix} \
    --covariates ${covariates_file} \
    --mode trans