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  • inconsistent between samtools mpileup output and bam tview

    Hi there,

    I have a question about the samtools mpileup and bam tview.

    By using the command "samtools mpileup -B test.bam > test.mpileup" (there is no difference for the output if adding the "-Q 0" paramter), I get the mpileup file which shows the base information for every nucletide position. For example: "chr3 54826891 N 3 att \e_".

    However, when I take a look at the bam file using tview (command "samtools tview test.bam genome.fa"), I notice that at the position chr3 54826891, the nucletides line up as "AaTtTt". All reads around the chromosome area seem to be aligned to the reference genome prefectly except for position 54826891, although I'm not able to view the quality score from tview of each base. I don't understand why the mpileup command drops some reads from the alignments.

    My question is, what's the criteria that the samtools mpileup process filters some base out? Should I trust the mpileup file or what's showing in the tview? I believe the following snp calling steps are based on the mpileup file instead of the raw alignments in the bam file, am I correct?

    Thanks,

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