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FiNGS- A New Software providing Filters for Next Generation Sequencing

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We use somatic variant callers to detect mutations in cancer samples by comparing sequencing data tumor and normal sample pairs. This is followed by some ad-hoc filtering that may produce low precision data resulting in a large number of false positives.

To overcome this issue, Wardell et al., [1] have developed a new software called FiNGS. This software filters somatic variants. It is a user-friendly tool that allows users to customize filters and thresholds. Users can also implement their own filtering strategies.

How does FiNGS work?

FiNGS takes BAM files of normal and tumor samples that are matched as input including a variants VCF file that enlists somatic mutations. It also takes another text file that mentions all filters and thresholds specified by the user. After processing, it outputs a VCF file along with other files that may be useful for the user [1].

FiNGS is platform-independent, easy to install, and written in Python3 which means it requires a minimum of Python3 version (Python 3.5 or higher) installed on your system. It can be downloaded via Bioconda, PyPi, or as a docker image. The source code is available on Github.

For more details, read here.


References

  1. Wardell, C.P., Ashby, C. & Bauer, M.A. (2021). FiNGS: high quality somatic mutations using filters for next generation sequencing. BMC Bioinformatics 22, 77.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

NGS

[Tutorial] Trailing of paired end reads using Trimmomatic tool in GALAXY.

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How to generate config file for docking using Autodock Tools?

Trimmomatic is a read trimming tool for Illumina NGS data [1]. It is a flexible tool providing several functions to be operated on reads. These functions include trailing, leading, and several other quality control operations. In this article, we are going to perform trailing on NGS paired-end reads data using the GALAXY platform [2]. (more…)

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NGS

How to extract methylation call using Bismark?

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How to extract methylation call using Bismark?

Bismark is bioinformatics to map bisulfite treated sequencing reads and to perform methylation calls [1]. In this article, we are going to extract methylation information from Bismark alignment outputs. (more…)

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NGS

Installing PANDAseq on Ubuntu

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Installing pandaseq on Ubuntu

PANDAseq is a bioinformatics tool that aligns paired-ends of Illumina sequences [1]. In this article, we are going to install PANDAseq on Ubuntu. (more…)

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