After the initial announcement at the American Society of Human Genetics, in October this year, the GENALICE team is working hard to rollout the new version of the GENALICE MAP NGS secondary data analysis suite, at all of its customer sites. With this new version (V2.4.0) the suite has greatly improved on various elements and expanded with new functional modules.
In short, the most important updates contain improvements in the basic toolset (Production Box) for single sample short read alignment and variant calling:
- Further variant detection accuracy improvements; INDEL call optimization
- Further footprint reduction of unmapped reads, resulting in even smaller GAR file sizes
- Full GRCh38 support of alternative section/contigs (e.g. distinct haplotypes, decoys) during read mapping
- HTTPS IO support to be able to run HIPAA compliant
- HTTP and S3 compatible logging and error report file handles
- Download of tutorials for training purposes
Like in earlier versions, V.2.4.0 will give its users access to the GAR toolbox. This toolbox contains the following functionalities:
- GAR API – providing access to the GAR through C & Java
- IGV plugin – to view the GAR directly
- GAR conversion tool (to BAM, SAM and FASTQ)
The Analysis Suite has been expanded with new functional modules. These modules are considered upgrades; hence they could be added to a standard license for single-sample alignment and variant calling.
POPULATION CALLING MODULE (already available as an upgrade option within V2.3.0, and now further advanced)
Advances in the unique Population Calling feature:
- Profile creation, e.g. a profile can be used as a cohort specific or targeted training set, to better detect known variants. While tools like GATK make use of generic training sets, GENALICE MAP offers users the opportunity to create e.g. race, native population or disease specific profiles. Such a profile allows for target call amplification and suppression, and results in better detection of known variants in the chosen population.
- Read pileup – The new pileup functionality is a GVM fed read mapping inspection tool. It quantifies coverage depths and variant counts directly from a GAR file.
SOMATIC CALLING MODULE (NEW in V2.4.0)
A method to distinct variants found in normal tissue from variants in a tumor sample, in order to identify tumor specific DNA mutations. In the Agbio industry, Somatic Calling can also be applied for the identification of new mutations to enhance breeding strategies while finding differentials between a target and base line.
COPY NUMBER VARIATION (CNV) MODULE (NEW in V2.4.0)
This newly released Copy Number Variation detection functionality uses a differential approach targeting tumor/normal pairs. Several filters can be applied to surface these areas that have a significant deviation from the expected coverage levels.
In case you would like to receive more information about and pricing of our GENALICE MAP NGS secondary data Analysis Suite, please let us know. Just give us a call or send an email us a call or send an email to email@example.com. We are happy to answer all of your questions.