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Only 60% overlap of SNP calling between bowtie and bwa

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  • Only 60% overlap of SNP calling between bowtie and bwa

    In recent days, I am analyzing a whole human genome sequencing Illumina data. I used bowtie (-n -m 2) and bwa (default) respectively, and found the overlap of SNP calling was 60%. So, anybody met the same situation? and what was wrong with it?

  • #2
    They work in a different way... bowtie doesn't allow indels in alignment and it may be missing a lot of SNP

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    • #3
      are your quality values illuimna/Sanger? if it is illumina, bowtie can get illumina quality (with the option --solexa1.3-quals) and then the output is Sanger quality.
      but in bwa, the quality of the output is like the input you give- without conversion. So make sure that after bowtie/bwa - you have the same quality format (which should be Sanger for Samtools and for many other applications).

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