What is BQSR?
BQSR stands for Base Quality Score Recalibration. In a nutshell, it is a data pre-processing step that detects systematic errors made by the sequencing machine when it estimates the accuracy of each base call.
What is somatic variant 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.
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 read genetic variants?
Variants are usually detected by reading the DNA code, a method called DNA sequencing. A proper report always contains the variant described on the DNA level. In addition, a report usually contains a description of the predicted consequence of the variant on the protein, rarely the consequence on RNA.
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 is a SNP call?
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 GATK spark?
Spark Follow. GATK Team. In a nutshell, Spark is a piece of software that GATK4 uses to do multithreading, which is a form of parallelization that allows a computer (or cluster of computers) to finish executing a task sooner. You can read more about multithreading and parallelism in GATK here.