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A SNP caller using next-generation sequencing data from multiple samples. MAFsnp has several features. First, MAFsnp can provide p-values with or without FDR correction for calling SNPs. Second, an estimated likelihood function is adopted to greatly speed up calling speed. Third, a novel distribution is proposed to accurately approximate the null distribution of the corresponding estimated likelihood ratio test statistic. Forth, MAFsnp is based on read count data, making it applicable to all types of sequence data. Fifth, MAFsnp avoids a tedious filtering procedure used in Bayesian methods.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
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Maintainer

  • Hong Zhang <zhanghfd at fudan.edu.cn>

Institution(s)

State Key Laboratory of Genetic Engineering and Institute of Biostatistics, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China

Funding source(s)

This work was supported by the State Key Development Program for Basic Research of China (grant number 2012CB316505) and the National Natural Science Foundation of China (grant number 11371101).

  • (Hu et al., 2015) MAFsnp: A Multi-Sample Accurate and Flexible SNP Caller Using Next-Generation Sequencing Data. PloS one.
    PMID: 26309201
  • (Mainzer et al., 2015) Isaac, the Illumina variant calling workflow. bioRxiv.
    DOI: 10.1101/031021
  • (Liu et al., 2013) Variant callers for next-generation sequencing data: a comparison study. PloS one.
    PMID: 24086590
  • (Nielsen et al., 2011) Genotype and SNP calling from next-generation sequencing data. Nature reviews Genetics.
    PMID: 21587300
  • (Altmann et al., 2012) A beginners guide to SNP calling from high-throughput DNA-sequencing data. Human genetics.
    PMID: 22886560
  • (Pabinger et al., 2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics.
    PMID: 23341494
  • (Yi et al., 2014) Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. Nucleic acids research.
    PMID: 24831545
  • (Pirooznia et al., 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human genomics.
    PMID: 25078893

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