What is Strelka2?

What is Strelka2?

Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor-normal sample pairs. The germline caller uses a tiered haplotype model to improve accuracy and provide read-backed phasing.

What is somatic calling?

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 are somatic variants?

Listen to pronunciation. (soh-MA-tik VAYR-ee-unt) An alteration in DNA that occurs after conception and is not present within the germline. Somatic variants can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to children.

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 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 variant calling pipeline?

Variant calls are generated from WGS data using a different pipeline than WXS and Targeted Sequencing samples.

What is germline DNA?

Germline DNA refers to tissue derived from reproductive cells (egg or sperm) that become incorporated into the DNA of every cell in the body of the offspring. A germline mutation may be passed from parent to offspring.

Can somatic cells become cancerous?

Somatic mutations can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to children. These alterations can (but do not always) cause cancer or other diseases.

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.

How do you call SNP?

SNP calling can be done using likelihood ratio tests or Bayesian procedures, in which the prior distributions for the allele frequencies are estimated from the data. Third, genotype calling should also proceed by combining data from multiple individuals in a Bayesian framework.