Search – Common Metabolic Diseases Genome Atlas

Software
released
Scalpel — source
Scalpel is a software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology (e.g., Illumina).
Software type: variant annotation
Software
released
GATK — source
The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data, developed by the Data Science and Data Engineering group at the Broad Institute. The toolkit offers a wide variety of tools, with a primary focus on
Software type: variant annotation
Software
released
AlleleSeq — source
Quantifies the allele-specific binding and expression at the SNP sites using the RNA-seq, ChIP-seq datasets, and diploid genome sequences.
Software
released
UES (Uncovering Enrichment through Simulation) — source
The UES (Uncovering Enrichment through Simulation) algorithm was written to help interpret results from genome-wide association studies (GWAS) using publicly available datasets.
Software type: variant annotation
Software
released
SeparateReadpairs — source
Splits up the interleaved file into two valid paired fastqs.
Software type: other
Software
released
vcf2diploid — source
Creates phased diploid genomes variants from a vcf file by integrating variants to a reference genome.
Software type: variant annotation