strkit 0.1.1

A toolkit for analyzing variation in short(ish) tandem repeats.

strkit

A toolkit for analyzing variation in short(ish) tandem repeats.

strkit call: Genotype caller with bootstrapped confidence intervals

A Gaussian mixture model tandem repeat genotype caller for long read data, tuned for high-fidelity long reads.

Features:

• Performant, vectorized (via parasail) estimates of repeat counts from high-fidelity long reads and a supplied catalog of TR loci.
• Parallelized for faster computing on clusters.
• 95% confidence intervals on calls via user-configurable bootstrapping.

Usage:

strkit call \
  path/to/read/file.bam \  # [REQUIRED] Indexed read file (BAM/CRAM)
  --ref path/to/reference.fa.gz \  # [REQUIRED] Indexed FASTA-formatted reference genome
  --loci path/to/loci.bed \  # [REQUIRED] TRF-formatted (or 4-col, with motif as last column) list of loci to genotype
  --min-reads 4 \  # Minimum number of supporting reads needed to make a call
  --min-allele-reads 2 \  # Minimum number of supporting reads needed to call a specific allele size 
  --flank-size 70 \  # Size of the flanking region to use on either side of a region to properly anchor reads

Slow performance can result from running strkit call or strkit re-call on a system with OpenMP, due to a misguided attempt at multithreading under the hood somewhere in Numpy/Scipy (which doesn't work here due to repeated initializations of the Gaussian mixture model.) To fix this, set the following environment variable before running:

export OMP_NUM_THREADS=1

strkit re-call: Genotype re-caller

This command has the same feature-set as strkit call, but is designed to be used with the output of other long-read STR genotyping methods to refine the genotype estimates when calling from HiFi reads.\

Features:

• Support for re-calling output from tandem-genotypes, RepeatHMM, and Straglr
• Strand resampling / bias correction (for use with the tandem-genotypes program)
• 95% confidence intervals on calls via user-configurable bootstrapping

Notes:

• --min-allele-reads will affect the confidence intervals given by the bootstrap process, especially in low-coverage loci. This should be set depending on the read technology being used; something like a single PacBio HiFi read generally contains higher-quality information than a single PacBio CLR read, for example.

strkit mi: Mendelian inheritance analysis

This tool is currently in development and in a very unfinished state. However, the following features will be in the final release:

• Mendelian inheritance % (MI) calculations for many common TR genotyping tools for both long/short reads
• Confidence-interval MI calculations for the genotyping tools which report CIs
• Reports of loci (potentially of interest) which do not respect MI

Copyright and License

Copyright (C) 2021-2022 David Lougheed & McGill University

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.