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  • elhb
    Junior Member
    • Dec 2009
    • 4

    -h flag of samtools mpileup

    Hi,

    I don't get how the homo-polymer error modelling works in samtools,
    could someone explain?

    in the manual it says:

    "-h INT Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. "

    does this mean that a lower INT will allow for more homopolymer errors or the other way around.

    Thanks
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283

    #2
    Originally posted by elhb View Post
    Hi,

    I don't get how the homo-polymer error modelling works in samtools,
    could someone explain?

    in the manual it says:

    "-h INT Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. "

    does this mean that a lower INT will allow for more homopolymer errors or the other way around.

    Thanks
    From my naive interpretation, if the INT*s/l is the error rate, then increasing INT would increase the error rate. Could you try a few different values around a known indel and a known hp and report back?

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