Lobstr-code

lobSTR: a short tandem repeat profiler for next generation sequencing data

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Overview

Code Changelog

New in version 4.0.6

Minor bug fixes and several new features:

New in version 4.0.0

The major change for this version is the ability for allelotype to take in BAM files from external aligners, mainly from BWA-MEM. This allows STR genotyping across large panels of samples that already have existing alignments for only a fraction of the computational cost of running the whole lobSTR pipeline. We have also added:

New in version 3.0.3

This version had minor changes.

New in version 3.0.2

This version has major algorithmic changes: we have removed the FFT period detection step and attempt to align STR-containing reads to all STRs at once, rather than only those with a specified motif. As a result, we have changed the index structure, and you will need to download a new index from the downloads page to use lobSTR 3. This new version significantly increases our alignment sensitivity.

lobSTR 3 usage remains largely the same. However we have made some significant additional improvements:

New in version 2.0.8

This version should have big alignment speedups compared to previous versions (up to 5-10x faster than before). This version also fixes a minor bug for an off-by-one error in how allele sequences are reported in the REF and ALT fields of the VCF file.

New in version 2.0.5

This version contains minor changes. Most notably we changed the way we package binaries, and the binaries should hopefully run smoothly on most systems.

New in version 2.0.4

New in version 2.0.3

New in version 2.0.2

New in version 2.0

Previous versions are available on github. Contact mgymrek AT mit DOT edu for versions before v2.0.2.

Index Changelog

Previous versions

Version 3 Version 2 (2.0.3+) Old lobSTR indices, compatible with version 2.0.0-2.0.2: