VEP determines the effect of variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

Runs SPIA to calculate the genotype distance between normal and tumor samples starting from the pilueps of the SNPs.

Analyzes genomic data from next-generation sequencing experiments. CLONETv2 offers a set of functions to compute allele specific copy number and clonality from segmented data leveraging heterozygous SNPs position pileups. The package also calculates the clonality of single nucleotide variants (SNVs) given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>. Prandi et al. (2019) <https://doi.org/10.1002/cpbi.81>

Runs segmentation using CVNKit and exports the copy number segments in a segfile.

Creates a genotype file based on the pileup of the SNPs and then runs EthSEQ.

Runs mutect2 variant calling and and variant filter.

PaCBAM is a C command line tool for the complete characterization of genomic regions and single nucleotide positions from next-generation sequencing data. PaCBAM implements a fast and scalable multi-core computational engine, generates exhaustive output files for downstream analysis, introduces an innovative on-the-fly read duplicates filtering strategy and provides comprehensive visual reports.

PaCBAM is a C command line tool for the complete characterization of genomic regions and single nucleotide positions from next-generation sequencing data. PaCBAM implements a fast and scalable multi-core computational engine, generates exhaustive output files for downstream analysis, introduces an innovative on-the-fly read duplicates filtering strategy and provides comprehensive visual reports.

Creates a genotype file starting from the pileup of the SNPs and then runs EthSEQ.

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. CollectHsMetrics is used to capture several metrics useful to verify the quality of target-capture sequencing experiments.

Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. CollectHsMetrics is used to capture several metrics useful to verify the quality of target-capture sequencing experiments.

Script that allows to merge a file (in tabular format) of variants annotated by VEP with the coverage information of the tumor and normal samples. In particular the script will add the coverage of reference and alternative bases and the allelic fractions at SNV positions in normal and tumor samples.