Lists (2)
Stars
A collection of scripts for filtering annotated variant call format files
ccastignani / ascat
Forked from VanLoo-lab/ascatASCAT copy number R package
Somatic copy variant caller (CNV) for next generation sequencing
Variant calling and somatic mutation/CNV detection for next-generation sequencing data
a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads
Copy number variant detection from targeted DNA sequencing
Conveniently perform ASCAT copy-number analysis from Tumor-Normal or Tumor only BAM files in R
Some extra scripts might be used during ChAMP DNA methylation analysis
MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
Molecular analysis of pre-invasive lung cancer samples
scripts to analyze and generate the figures for the methyl-seq platform comparison article
Tools (written in C using htslib) for manipulating next-generation sequencing data
bedtools - the swiss army knife for genome arithmetic
Tools to handle reads sequenced with unique molecular identifiers (UMIs).
Tools for handling Unique Molecular Identifiers in NGS data sets
The use of UMIs for sequencing becomes more and more frequently used so we need to take them into consideration when deduplicating data aligning to the same positions
DNA sequencing analysis notes from Ming Tang
DNANexus Whole Genome Bisulphite Analysis Pipeline