What it does

This tool is used to convert informative read depth (specified by user) to sequencing depth when the STRs is mapped using STR-FM pipeline. The locus specific sequencing depth (yrequired) is the sequencing depth that will make an STR locus to have a certain informative read depth based on uniform mapping of reads. It is calculated as follows:

yrequired = ( X * L ) / (L - (2F+r-1))

where X = informative read depth, L = read length, F = the number of flanking bases required on either side, r = the expected repeat length of the STR of interest.

The genome wide sequencing depth is the sequencing depth that will make certain percentage of genome (e.g. 90 percent or 95 percent) to have certain locus specific sequencing depth. It's calculated using numerical guessing to find smallest lambda that:

        0.90 (or other proportion specified by user) < = P(Y=0) + P(Y=1) + …+ P(Y=yrequired-1)

        where P(Y=y) = (lambda^(y) * e ^(-lambda)) /y!

y = specific level of sequencing depth. Lambda = genome wide sequencing depth

Please refer the Methods section of the paper cited below for further details.

Citation

When you use this tool, please cite Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research