What it does

• This tool will combine the read profile probabilities for each allele combination in the input and calculates the probability to detect heterozygote for each allele combination and each depth.

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

Input

The input format is the same as output from Evaluate the probability of the allele combination to generate read profile tool.

• Column 1 = location of STR locus.
• Column 2 = length profile (length of STR in each read that mapped to this location in comma separated format).
• Column 3 = motif of STR in this locus. The input file can contain more than three columns.
• Column 4 = homozygote/heterozygote label.
• Column 5 = log based 10 of (the probability of homozygote/the probability of heterozygote)
• Column 6 = Allele for most probable homozygote.
• Column 7 = Allele 1 for most probable heterozygote.
• Column 8 = Allele 2 for most probable heterozygote.
• Column 9 = Probability of the allele combination to generate given read profile.
• Column 10 = Number of possible rearrangement of given read profile.
• Column 11 = Probability of the allele combination to generate read profile with any rearrangement (Product of column 9 and column 10)
• Column 12 = Read depth

Only columns 2,3,4,7,8,11 were used in calculation.

Output

The output will contain the following header and columns

• Line 1 header: read_depth allele heterozygous_prob motif
• Column 1 = read depth
• Column 2 = allele combination
• Column 3 = probability to detect heterozygote of that allele combination
• Column 4 = motif