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  • mean position of the variant within the variant supporting reads

    Hi,

    I am trying to call SNPs using SAMtools mpileup. I am interesting in determining the mean position of the variant within the variant supporting reads. I know there is the -O command which gives: output base positions on reads

    Firstly I am not 100% positive what 'mean position' refers to and secondly, while the -O command gives output base positions on reads, how would I determine the mean position within the variant supporting reads?

    Any help would be much appreciated.

    Thank you.

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