Changes The GnomAD resource is now optional, in case it is not available or you don't trust how it is used. When --gnomad is not provided then the contamination estimation steps are skipped. Also the filtering of common germline mutations is disabled. As an alternative a contamination estimate can be provided through --args_filter "--contamination-estimate 0.2
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
updated gtt-hmms to count properly when hmm profile doesn't have accessions in it incorporated exit ...
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Changes Fixes #26 and #41 by annotating VCFs with homoplasmic problematic sites from DeMaio. These ...
Changes Support for single sample through CLI parameters --input_name, --input_tumor_bam and --inpu...
Changes: Memory and CPUs are now parametrised more granularily Analysis intervals are now optional ...
Changes Add support for STAR for RNA-seq alignment Record software versions in the samples outpu
Changes Integrate pangolin for lineage determination. Integrate VAFator to annotate mutations with ...
Major changes: Add coverage analysis for FASTQ pipeline Add Pfam domain annotations in the outpu...
Changes Adds an optional step to trim primers when a bed with primer regions is provided with --pri...
Changes: Add support for replicates in Mutect2 Improve tests to check output file
Major changes Add read trimming with fastp Output QC results in JSON format Integrate 4 variant...
This dataset contains processed files from gnomAD that can be used with GREEN-VARAN. These files rep...
We are happy to announce the release of SnakeMAGs v1.1.0 which features two major improvements. The ...
Changes Integration of funcotator as an optional final step. Output in VCF and MAF formats Argument...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
updated gtt-hmms to count properly when hmm profile doesn't have accessions in it incorporated exit ...
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Changes Fixes #26 and #41 by annotating VCFs with homoplasmic problematic sites from DeMaio. These ...
Changes Support for single sample through CLI parameters --input_name, --input_tumor_bam and --inpu...
Changes: Memory and CPUs are now parametrised more granularily Analysis intervals are now optional ...
Changes Add support for STAR for RNA-seq alignment Record software versions in the samples outpu
Changes Integrate pangolin for lineage determination. Integrate VAFator to annotate mutations with ...
Major changes: Add coverage analysis for FASTQ pipeline Add Pfam domain annotations in the outpu...
Changes Adds an optional step to trim primers when a bed with primer regions is provided with --pri...
Changes: Add support for replicates in Mutect2 Improve tests to check output file
Major changes Add read trimming with fastp Output QC results in JSON format Integrate 4 variant...
This dataset contains processed files from gnomAD that can be used with GREEN-VARAN. These files rep...
We are happy to announce the release of SnakeMAGs v1.1.0 which features two major improvements. The ...
Changes Integration of funcotator as an optional final step. Output in VCF and MAF formats Argument...
Non functional changes Migrate workflow to DSL 2 Make conda dependencies more granular Improve test
updated gtt-hmms to count properly when hmm profile doesn't have accessions in it incorporated exit ...
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...