QTLtools-extract1
Data extraction mode.
Usage
QTLtools extract
[--vcf
--bed
--cov]
relevant_file
--out
output_prefix
[OPTIONS]
Overview
Extract all the data from the provided files into one flat file. This will also impute all the missing data.
Options
-
--vcf [in.vcf|in.bcf|in.vcf.gz] -
Genotypes in VCF/BCF format. At least one of --vcf --bed --cov is REQUIRED.
-
--bed quantifications.bed.gz -
Molecular phenotype quantifications in BED format. At least one of --vcf --bed --cov is REQUIRED.
-
--cov covariates.txt -
Covariates data. At least one of --vcf --bed --cov is REQUIRED.
-
--out filename_prefix -
Output file name prefix. REQUIRED.
-
--region chr:start-end -
Genomic region to be processed. E.g. chr4:12334456-16334456, or chr5.
Output files
|
Flat file with samples in rows and all the extracted variables in columns. |
|---|---|
|
Genomic locations of the extracted variables. |
Examples
- o
-
Extract genotypes, gene quantifications, and covariates from a certain region:
-
QTLtools extract --vcf genotypes.chr22.vcf.gz --bed genes.50percent.chr22.bed.gz --cov genes.covariates.pc50.txt.gz --region chr22:17000000-18000000 --out extract_output
Citation
Delaneau, O., Ongen, H., Brown, A. et al. A complete tool set for molecular QTL discovery and analysis. Nat Commun 8, 15452 (2017). <https://doi.org/10.1038/ncomms15452>
Releases
Unchanged in 3 releases since Debian 11 (Bullseye).