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  2. High-throughput sequencing
  3. Whole-genome sequencing
  4. Germline SNP detection
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A probabilistic framework for the discovery of single nucleotide variants in WGSS data.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS
Programming languages:
C
Computer skills:
Advanced
Stability:
Stable
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  • (Crisan et al., 2012) Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors. PloS one.
    PMID: 22916110
  • (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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