Tool: Somaticsniper - Variant Caller Used For Somatic Snvs And Indels
gravatar for Malachi Griffith
8.3 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

Somatic Sniper is a variant caller used to identify somatic SNVs and Indels by comparison of a tumor normal pair.

SomaticSniper: Identification of Somatic Point Mutations in Whole Genome Sequencing Data

From the SomaticSniper website:

The purpose of SomaticSniper program is to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent with how the SAM format reports such probabilities. It is currently available as source code via github or as a Debian APT package.

SomaticSniper User Manual

somatic variant tool • 3.4k views
ADD COMMENTlink modified 8.2 years ago by Istvan Albert ♦♦ 85k • written 8.3 years ago by Malachi Griffith18k
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