Downstream Pipelines
Downstream pipelines use analysis-ready bam files to generate filtered lists of variants in vcf format.
These bam files are standard alignment files that have been further processed to eliminate duplicate reads and recalibrate base quality scores as described here.
Germline
Germline pipelines are designed to identify rare inherited variations in an individual’s genome. These mutations may be present in the individual’s parents or may arise as new mutations in germ cells and be passed on as de novo mutations.
Somatic
Somatic pipelines are designed to identify somatic mutations, which are changes that occur in an individual’s DNA during their lifetime and are present in certain cells only. These mutations are often associated with cancer and can be identified using matched tumor-normal samples or tumor-only data in order to discover mutations that may be related to cancer development or progression.