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  • snp calling with bwa-samtools

    hi,everyone! I do wet experiment verification for my heterozygous snp found by bwa-samtools in rice genome recently,however only three of fourteen got experiment support, the rest didn't get! I have checked the reads coverage in the position of SNPs, all the indication are that they are SNPs!
    Could someone explain that?

    all the reply are appreciated!

  • #2
    1. Sequencing error
    2. Mapping error
    3. Validation error.

    Those are 3 possibilities, I'm sure there are more. You don't provide much info so it's hard to know for sure.

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    • #3
      i also meet the problem,can we have a chat? my email:[email protected] QQ:872664567

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      • #4
        Hello heiya, my experience is that using samtools with default settings will give you a high number of false positives, this could be what you are seing.

        You could try running snp-calling with the GATK using the built-in recalibration options. GATK has quite a low number of false positives. Compare the results from GATK with your existing results, and see what you get.

        Ø

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