bcftoolscsq
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:
Value |
Description |
|---|---|
a |
Take GTs as is, create haplotypes regardless of phase (0/1 → 0|1) |
m |
Merge all GTs into a single haplotype (0/1 → 1, 1/2 → 1) |
r |
Require phased GTs, throw an error on unphased heterozygous GTs |
R |
Create non-reference haplotypes if possible (0/1 → 1|1, 1/2 → 1|2) |
s |
Skip unphased heterozygous GTs |
$ pbrun bcftoolscsq \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-file input_file.vcf.gz
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
Predict consequences from variants in VCF file.
Input/Output file options
- --in-file IN_FILE
- --ref REF
- --out-file OUT_FILE
- --gff-annot GFF_ANNOT
Path to the input vcf file. (default: None)
Option is required.
Path to the reference file in fasta format. (default: None)
Option is required.
Path of the output file. If this option is not used, it will write to standard output. (default: None)
GFF3 annotation file, such as ftp://ftp.ensembl.org/pub/current_gff3/homo_sapiens
(default: None)
Option is required.
Tool Options:
- --phase PHASE
- --local-csq
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
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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.
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.