inSTRbility

inSTRbility is a toolkit to analyse somatic instability at tandem repeat loci from whole genome sequencing datasets.

The tools includes two modules:

1. extract: Extracts reads mapping to repeat loci and records variations within the repeat region along with SNPs outside of the repeat. The output is a tab-delimited file with information about each read including allele length, haplotype, and methylation information.

2. model: Models the read allele length distribution at each locus to estimate the instability of the repeat locus based on the extracted reads.

The basic pipeline of the tool includes fetching reads mapping to repeat region and recording variations within the repeat region along with SNPs outside of the repeat. The variations falling within the repeat region contribute towards calculation of the allele length in the read. Based on the SNP the reads are segregated into two haplogroups. The allele length for each group is calculated as the mode of the group. For each read instability is calculated as the mean absolute deviation from the allele length.

NOTE: The tool currently works on long read sequencing datasets including PacBio and ONT.

Installation

git clone https://github.com/dashnowlab/inSTRbility.git

cd inSTRbility

python setup.py install

Usage for extract

Printing help

$ python ./inSTRbility/extract_reads.py -h

Basic usage

$ python ./inSTRbility/extract_reads.py -ref [fasta] -bed [regions_file] -bam [aln_file] -o [output_file] --reads-out

Usage for model

Basic usage

$ python ./inSTRbility/calc_instability.py -i [input_file] -o [output_file] [-v [vcf_file]]

Input TSV file

The input file for the instability calculation is a tab-delimited file with the following columns:

Column	Description
chromosome	Chromosome
start	Start position
end	End position
individual	Sample ID
repeat motif	Repeat motif
read_id	Read ID
haplotype	Haplotype ID
allele_length	Allele length in the read
sequence	Sequence of the repeat locus in the read. Optional:
avg_meth	Average methylation in the repeat locus in the read
nmeth_bases	Number of methylated bases in the repeat locus in the read

Mutation model for calculating instability

inSTRbility models the read distribution of a repeat locus based on a compound negative binomial geometric distribution. The model is fitted to the read distribution and the parameters are used to calculate the instability of the locus. The model uses the geometric distribution to the model the size of the expansion or contraction step size in each mutation event. The model uses the negative binomial distribution to model the number of mutation events in a cell lineage at a given locus.

Scripts for extracting reads

• __init__.py
• extract_reads.py
• cigar_utils.py
• cstag_utils.py
• md_utils.py
• genotype_utils.py
• phasing_utils.py
• instabillity_utils.py
• process_reads.py
• locus_utils.py
• operation_utils.py
• version.py

Scripts for modelling instability

• calc_instability.py
• parse_inputs.py
• suggest_re_rc_grid.py
• nbgeom_modelling.py
• compress_bed.py
• calibrate.py
• check_lock.py
• multisample-analysis.py