Publication date
October 2022
DOIAbstract
Changes Add support for STAR two pass mode which increases sensitivity in novel splice junctions Add additional arguments for BWA mem, BWA mem 2 and STAR that enables the user to add any additional argument
Changes Add support for STAR two pass mode which increases sensitivity in novel splice junctions Add additional arguments for BWA mem, BWA mem 2 and STAR that enables the user to add any additional argument
Changes: Add support for single samples using --input_fastq1 and --input_fastq
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descript...
Supplementary Figure 1:Alignment of human TRPM channels 1-8 amino acid sequences (UniProt accession ...
Changes Add support for STAR for RNA-seq alignment Record software versions in the samples outpu
Changes Add STAR for alignment of RNA-seq data Record software versions in the output Repository ha...
Changes Performance improvement by merging the last two steps (SnpEff and bgzip/tabix) into a singl...
Changes Support for single sample through CLI parameters --input_name, --input_tumor_bam and --inpu...
Changes: Number of required parametrised on --cpus, default 8 Memory required parametrised on --...
First pre-release integrating alignment, mark duplicates, realignment around indels, variant calling...
Changes Replace Picard mark duplicates by sambamba Remove unnecessary sort operation Limits memory ...
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descript...
Updates Added Biopython SeqIO functionality for Stockholm file parsing - see ssAlign.py. This remov...
Changes: add support for a single input BAM file fix realignment step when no known indels are p...
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descript...
Changes: Add support for single samples using --input_fastq1 and --input_fastq
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descript...
Supplementary Figure 1:Alignment of human TRPM channels 1-8 amino acid sequences (UniProt accession ...
Changes Add support for STAR for RNA-seq alignment Record software versions in the samples outpu
Changes Add STAR for alignment of RNA-seq data Record software versions in the output Repository ha...
Changes Performance improvement by merging the last two steps (SnpEff and bgzip/tabix) into a singl...
Changes Support for single sample through CLI parameters --input_name, --input_tumor_bam and --inpu...
Changes: Number of required parametrised on --cpus, default 8 Memory required parametrised on --...
First pre-release integrating alignment, mark duplicates, realignment around indels, variant calling...
Changes Replace Picard mark duplicates by sambamba Remove unnecessary sort operation Limits memory ...
Changes Upgraded GATK version to 4.2.5.0 (see release notes https://github.com/broadinstitute/gatk/...
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descript...
Updates Added Biopython SeqIO functionality for Stockholm file parsing - see ssAlign.py. This remov...
Changes: add support for a single input BAM file fix realignment step when no known indels are p...
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descript...
Changes: Add support for single samples using --input_fastq1 and --input_fastq
Annotation of mutated peptide sequences (mps) with published or novel potential neo-epitope descript...
Supplementary Figure 1:Alignment of human TRPM channels 1-8 amino acid sequences (UniProt accession ...
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