This is a modified version of the original Straglr tool which focuses on genotyping of clinical tandem repeat(TR) expansions from targeted or whole genome long-read alignments.
Straglr is implemented in Python 3.8 and has been tested in Linux environment.
Straglr depends on Tandem Repeat Finder(TRF) for identifying TRs and blastn for iotif matching. (TRF and blastn executables must be in $PATH). Other Python dependencies are listed in requirements.txt.
The file environment.yaml can by used by conda to create an environment with all dependencies installed:
mamba env create --name straglr --file=environment.yaml
conda activate straglr
pip install git+https://github.com/philres/straglr.git#egg=straglr
conda activate straglr
straglr-genotype --loci repeat-annotation/hg38/clinical_repeats.bed --sample <sample name> --vcf <output vcf> --sex <male/female> input.bam reference.fasta
Long read alignments sorted by genomic coordindates in BAM format against the reference genome. Suggested aligner: Minimap2 -- Please use the option -Y to enable soft-clipping so that read sequences can be assessed directly from the BAM file.
usage: straglr-genotype [-h] --vcf VCF [--tsv TSV] [--threads THREADS] --sample SAMPLE [--sex {male,female}] --loci LOCI [--min_support MIN_SUPPORT] [--min_cluster_size MIN_CLUSTER_SIZE] [--genotype_in_size] [--max_cov MAX_COV] [--trf_args Match Mismatch Delta PM PI Minscore MaxPeriod] [--working_dir WORKING_DIR]
[--tmpdir TMPDIR] [--debug] [--version]
bam genome_fasta
positional arguments:
bam bam file
genome_fasta genome_fasta
options:
-h, --help show this help message and exit
--vcf VCF, -v VCF Path to output VCF file.
--tsv TSV Output per read stats to TSV file.
--threads THREADS, -t THREADS
Number of processes
--sample SAMPLE Sample name to use in output VCF file
--sex {male,female} Sex of sample
--loci LOCI bed file of loci for genotyping
--min_support MIN_SUPPORT
minimum number of supporting reads for detecting expansion. Default:2
--min_cluster_size MIN_CLUSTER_SIZE
minimum number of supporting reads for allele clustering. Default:2
--genotype_in_size report genotype in size instead of copy numbers
--max_cov MAX_COV maximum allowed coverage for ins inspection. Default:1000
--trf_args Match Mismatch Delta PM PI Minscore MaxPeriod
tandem repeat finder arguments. Default:2 5 5 80 10 10 500
--working_dir WORKING_DIR
working directory. Default:current directory
--tmpdir TMPDIR directory to use for generating tmp files instead of system TEMP
--debug debug mode i.e. keep trf output
--version show program's version number and exit
- VCF file
- TSV file - detailed output one support read per line
- chrom - chromosome name
- start - start coordinate of locus
- end - end coordinate of locus
- repeat_unit - repeat motif
- genotype - copy numbers (default) or sizes (
--genotype_in_size) of each allele detected for given locus, separate by semi-colon(";") if multiple alleles detected, with number of support reads in bracket following each allele copy number/size. An example of a heterozygyous allele in size:990.8(10);30.9(10) - read - name of support read
- copy_number - number of copies of repeat in allele
- size - size of allele
- read_start - start position of repeat in support read
- allele - allele that support read is assigned to
Chiu R, Rajan-Babu IS, Friedman JM, Birol I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol 22, 224 (2021). https://doi.org/10.1186/s13059-021-02447-3