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  • Aligner/SNP caller for Illumina data

    Hi,

    to keep the number of false-positive-SNP-calls and thus the number of follow-up experiments (e.g. sanger control sequencing) as low as possible, I was wondering which software performs best on this task.

    Fungi, human (enriched) datasets.

    What are the experiences?

    I surely will try a few, including Illumina's CASAVA, but some hints are welcome ..

    Thanks,
    Sven

  • #2
    We had exactly the same problem, but with plant transcriptomes. To solve it we developed a software named ngs_backbone. Even if you do not use this software you could take a look at the filters that we applied to look for the more promising SNPs.
    Regards,

    Jose Blanca

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    • #3
      Thanks, Jose, I will surely have a look at 'ngs_backbone' and the filters used.

      Sven

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