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]
                        [--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

--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