Version 1.3.7

This is a bugfix to VariantQC. It fixes the 'Comparison method violates its general contract!' that could occur when processing certain types of input VCFs.

Version 1.3.6

This expands support for the tool PrintReadBackedHaplotypes, which inspects a BAM over the provided list of intervals. For each interval (which is typically short), the tool calculates all unique sequences (based on the raw forward/reverse reads) and reports of table with the number of read pairs for each. This was designed for applications like reconstructing haplotypes over a CRISPR-edited region.

Version 1.3.5

This version improves the speed of VariantQC multithreading

Version 1.3.4

This release includes several improvements to VariantQC:

• Contigs are sorted by numeric order in the HTML report
• VariantQC can be executed using multiple VCFs as input. This is a beta feature with limited testing.
• Adds new --threads argument for multi-threading

Version 1.3.3

This is a minor release for IntegrationSiteMapper, which adds the ability to filter alignments based on MAPQ and defaults to ignore multi-mapping reads (MAPQ=0).

Version 1.3.2

This is a minor release that includes a fix for VariantQC when the source genome has has contigs, but -maxContigs is used ignore smaller contigs. Now, VariantQC groups these variants into a new level 'Other' which allows them to be included in the report without 100s or 1000s of stratification levels.

Version 1.3.1

This is a minor release that includes a bugfix to ClipOverlappingAlignments, which caused an overclip by 1bp for alignments terminating in the interval region(s)

Version 1.30

This release renames the tool TagPcrSummary to IntegrationSiteMapper, reflecting that it is a more general purpose tool that could be used on many library types.

Version 1.29

This version adds more custom variant annotations to DiscvrVariantAnnotator, including MendelianViolationCount and MendelianViolationBySample, each of which summarize MVs per site.

Version 1.28

Add VcfComparison, a tool for site and genotype level comparisons between VCFs