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Hi, I am a beginner working on SNP callings. I am trying samtools mpileup and it works pretty cool. However, I have no idea about the parameters and I am thinking which parameters control the output variance report. I can collect all the variances even that is sequencing error instead of SNPs. Thanks!
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Hi,
The samtools webpage has quite detailed explanation on the parameters. Here is the link: http://samtools.sourceforge.net/samtools.shtml.
Best regards,
Douglas
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