-h flag of samtools mpileup

[elhb]

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]

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?