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  • little mutations were found by samtools mpileup

    HI:
    I used samtools mpileup to to find mutations. My sample genome is relative small and the coverage is about 1000X (illumina paired-end 90bp)

    I used following code to generate VCF:
    samtools view -bS sample.sam > sample.bam#generate bam
    samtools sort sample.bam sample.sorted.bam#sort bam
    samtools mpileup -ugf sample.fas sample.sorted.bam | bcftools view -vcg > sample.vcf#generate VCF file

    In my vcf output, There are just two mutations, but I visulized the sam file in IGV and found lots of mutations. I supposed those mutations is filter out because of bad qc, So I used "-Q 0 -q 0 -C 0" but no more mutations were found.
    Are there other parameters I didn`t found?

    Any sugestions will be appreciated!
    Last edited by tujchl; 06-07-2012, 06:10 PM.

  • #2
    Try

    samtools mpileup -Bugf sample.fas sample.sorted.bam | bcftools view -vcg > sample.vcf#generate VCF file
    Sometimes, the BAQ corrections kill good mutations.

    Comment


    • #3
      Thank you for your reply, I try -B, but no more mutations were found.
      Any one know what`s wrong?
      The version of samtools is 0.1.18 (r982:295)

      Comment

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