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How to analyse the result of GATK by using the VarScan

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  • How to analyse the result of GATK by using the VarScan

    Dear all,
    I have one sample genome sequence data which mapped into the reference genome, and I have called the SNP with GATK. However, its seems the GATK can only calling the SNP between sample and reference, but I want to calling the SNP among sample. And I try to analyse the result of GATK by using the VarScan, but its failure! Is there any softwares can do this job?
    Thanks!

  • #2
    Dear qingmei,

    You can perform multi-sample SNP calling with a few different tools including SAMtools mpileup.

    You can also analyze raw mpileup from multiple samples with VarScan as follows:

    samtools mpileup -f reference.fa -q 1 sample1.bam sample2.bam sample3.bam >out.mpileup
    java -jar VarScan.jar mpileup2snp out.mpileup >out.mpileup.snp

    Sincerely,

    Dan Koboldt

    Comment


    • #3
      Dear Dan,
      Thank you very much for your help. The samtools can do the job, but I want to use the GATK soft which have the function of Base Quality Recalibration and Variant Recalibration for SNP calling. So, I want to know whether have methods to call the SNP among sample by using the GATK soft.
      Thanks!

      Comment

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