Command-line interface

strvcf-annotator

Annotate STR regions in VCF files using a BED file

usage: strvcf-annotator [-h] (--input INPUT | --input-dir INPUT_DIR) --str-bed
                        STR_BED (--output OUTPUT | --output-dir OUTPUT_DIR)
                        [--verbose] [--somatic-mode]
                        [--ignore-mismatch-warnings] [--jobs JOBS]
                        [--mismatch-truth {panel,vcf,skip}] [--version]

Named Arguments

--input

Path to input VCF file

--input-dir

Directory containing input VCF files

--str-bed

Path to BED file with STR regions (CHROM, START, END, PERIOD, RU)

--output

Path to output VCF file (for single file mode)

--output-dir

Directory for output VCF files (for batch mode)

--verbose, -v

Enable verbose logging

Default: False

--somatic-mode

Enable somatic filtering: skip variants where both samples have identical genotypes

Default: False

--ignore-mismatch-warnings

Suppress warnings about reference mismatches between STR panel sequence and VCF REF allele.

Default: False

--jobs

Number of parallel jobs to use for processing. Each job processes one VCF file. If not specified, the number of jobs is automatically determined based on CPU cores, number of files, and available RAM.

--mismatch-truth

Possible choices: panel, vcf, skip

Which source to treat as ground truth when a mismatch is detected: ‘panel’ (default), ‘vcf’, or ‘skip’ (skip mismatching loci).

Default: 'panel'

--version

show program’s version number and exit

Examples:

# Annotate single VCF file strvcf-annotator –input input.vcf –str-bed repeats.bed –output output.vcf

# Batch process directory strvcf-annotator –input-dir vcf_files/ –str-bed repeats.bed –output-dir annotated/

# Enable verbose logging strvcf-annotator –input input.vcf –str-bed repeats.bed –output output.vcf –verbose

# Somatic mode (filter variants where tumor==normal genotypes) strvcf-annotator –input somatic.vcf –str-bed repeats.bed –output output.vcf –somatic-mode

# Suppress mismatch warnings and trust VCF reference when mismatch happens strvcf-annotator –input input.vcf –str-bed repeats.bed –output output.vcf

–ignore-mismatch-warnings –mismatch-truth vcf