Predict consequences from variants in a VCF file.

The input VCF file can be either uncompressed .vcf or gzipped .vcf.gz. The output will be uncompressed.

The --phase option accepts one of the following values:




Take GTs as is, create haplotypes regardless of phase (0/1 → 0|1)


Merge all GTs into a single haplotype (0/1 → 1, 1/2 → 1)


Require phased GTs, throw an error on unphased heterozygous GTs


Create non-reference haplotypes if possible (0/1 → 1|1, 1/2 → 1|2)


Skip unphased heterozygous GTs

Quick Start

$ pbrun bcftoolscsq \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --in-file input_file.vcf.gz

Compatible Baseline Command

This Parabricks command:

$ pbrun bcftoolscsq \
    --in-file input.vcf \
    --out-file outcsq.vcf \
    --ref refseq.fa \
    --gff-annot Homo_sapiens.GRCh38.105.chr.gff3

Will produce the same results as this bcftools command:

$ bcftools csq -f refseq.fa -g Homo_sapiens.GRCh38.105.chr.gff3 input.vcf -Ov -o out.bcf

bcftoolscsq Reference

Predict consequences from variants in VCF file.

Input/Output file options

--in-file IN_FILE

Path to the input vcf file. (default: None)

Option is required.

--ref REF

Path to the reference file in fasta format. (default: None)

Option is required.

--out-file OUT_FILE

Path of the output file. If this option is not used, it will write to standard output. (default: None)

--gff-annot GFF_ANNOT

GFF3 annotation file, such as ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens

(default: None)

Option is required.

Tool Options:

--phase PHASE

Determines the handling of unphased heterozygous genotypes. Options are: a|m|r|R|s. See documentation for details. (default: None)


Switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time.

(default: None)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)


Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.


Do not override seccomp options for docker (default: None).


View compatible software versions.