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  • varscan mpileup2__ or pileup2__

    Hello,

    I'm a new user of VarScan. I am working with pooled samples (pools of 25) thus my samtools mpileup file represents a "single sample" in the sense that all reads in the bam file are treated together but "multiple samples" in the sense that the output from the samtools mpileup command summarizes reads from multiple individuals.*

    I am wanting to use VarScan to make consensus calls. Unlike the pileup2cns command, the mpileup command seems to output exactly what I want (output in vcf format and list all positions, not just variants; as well as allows from strand filtering). But I'm wondering if it is inappropriate to use this command when the mpileup is from a single bam file (it doesn't in practice throw any errors but are there any problems with using the suite of mpileup2__ commands on a mpileup from a single bam)? Is the only difference between the commands that mpileup2cns has the ability to make calls based on multiple samples or are there other important differences?

    Thanks in advance for the help!

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