What is FreeBayes?

FreeBayes is a genetic variant detector designed to find small polymorphisms (SNPs, indels, MNPs and complex events). FreeBayes is haplotype-based, in the sense that it calls variants based on the literal sequences of reads aligned to a particular target, not their precise alignment.

What is Mutect2?

Given a matched normal, Mutect2 is designed to call somatic variants only. The tool includes logic to skip emitting variants that are clearly present in the germline based on provided evidence, e.g. in the matched normal. This is done at an early stage to avoid spending computational resources on germline events.

What is somatic variant calling?

Summary. The somatic variant caller is a powerful new tool for the analysis of cancer samples and can detect mutations below 5% frequency with high-quality sequencing from the MiSeq system and the TruSeq Amplicon – Cancer Panel.

What type of mutations are tools like SAMtools currently not able to detect?

SAMtools, however, is not able to call any variants with allelic frequencies below 0.20 in the first dataset. Regarding the tools that already called variants at VAF ≤ 0.05, sensitivity is in most cases close to 1.00 if variants at higher allelic frequencies are considered.

What is DeepVariant?

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. This tutorial explains how to run DeepVariant on Google Cloud using sample data. You run DeepVariant on a single Compute Engine instance.

What is in a VCF file?

VCF is a text file format (most likely stored in a compressed manner). It contains meta-information lines, a header line, and then data lines each containing information about a position in the genome. There is an option whether to contain genotype information on samples for each position or not.

How can I speed up my Mutect2?

To increase the speed of a Mutect2 workflow, consider running multiple instances of Mutect2 with e -L (or –intervals ) option, with an included BED file of genomic regions. A target list of 10,000 regions could then be broken up into groups of 100-regions and run in parallel.

What is SNP calling?

SNP calling aims to determine in which positions there are polymorphisms or in which positions at least one of the bases differs from a reference sequence; the latter is also sometimes referred to as ‘variant calling’.

What is the difference between germline and somatic variant calling?

Germline pathogenic variants are identified through a blood sample or with buccal cells from a saliva sample. Somatic variants are detected by either testing the tumor directly or liquid biopsy of a blood sample with circulating tumor cells to identify the DNA sequencing changes driving tumor growth.

What does samtools view do?

The samtools view command is the most versatile tool in the samtools package. It’s main function, not surprisingly, is to allow you to convert the binary (i.e., easy for the computer to read and process) alignments in the BAM file view to text-based SAM alignments that are easy for humans to read and process.

What is a BCF file bioinformatics?

The BIM Collaboration Format (BCF) is a structured file format suited to issue tracking with a building information model. BCF is designed primarily for defining views of a building model and associated information on collisions and errors connected with specific objects in the view.

What is NA12878?

In 2015, NIST released the pilot genome Reference Material 8398, which is genomic DNA (NA12878) derived from a large batch of the Coriell cell line GM12878, characterized for high-confidence SNPs, indel, and homozygous reference regions (Zook, et al., Nature Biotechnology 2014 and Zook, et al., Nature Biotechnology …

What is the difference between varscan and varscan2?

In contrast, VarScan employs a robust heuristic/statistic approach to call variants that meet desired thresholds for read depth, base quality, variant allele frequency, and statistical significance. Varscan2 is coded in Java, and should be executed from the command line (Terminal, in Linux/UNIX/OSX, or Command Prompt in MS Windows).

What does @varscan2 detect in exome data?

VarScan2 detects somatic mutations and copy number alterations (CNAs) in exome data from tumor–normal pairs. Bioinformatics, 2009, 25 (17), pp.2283-2285.

Is there a docker implementation of the varscan2 CNV caller?

This repository contains code to create a docker implementation of the Varscan2.4.2 copynumber variation (CNV) caller. Varscan2 was developed by Dan Koboldt (see References below). It can be used to detect copy number variation (CNV) in sample pairs, usually exomes from a tumor and control from one patient.

What is the trio-calling module for varscan?

We have developed a trio-calling module for VarScan which leverages the family relationship to improve variant calling accuracy, identify apparent Mendelian Inheritance Errors (MIEs), and detect high-confidence de novomutations.