ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity outside of ROHs. ROHan can work on modern and ancient samples with signs of ancient DNA damage.
ROHan can work for sample with depth-of-coverage 4-5X or above for modern samples and 7-8X for damaged ancient samples. It makes the following assumptions:
The per-base quality scores are sufficiently representative of the error rate, this should be the case for most modern Illumina runs.
Inbreeding is sufficiently recent. ROHan cannot deal with very distant and continuous inbreeding.
For ancient samples, you have adequately quantified the rates of ancient DNA damage (see README).
Use the module name rohan to discover versions available and to load the application.
[]$ bam2prof Usage bam2prof <options> [in BAM file] This program reads a BAM file and produces a deamination profile for the 5' and 3' ends Other options: -minq Require the base to have at least this quality to be considered (Default: 0) -minl Require the base to have at least this quality to be considered (Default: 35) -endo Require the 5' end to be deaminated to compute the 3' end and vice-versa (Default: 0) -length [length] Do not consider bases beyond this length (Default: 5 ) -err [error rate] Substract [error rate] from the rates to account for sequencing errors (Default: 0 ) -log Print substitutions on a PHRED logarithmic scale (Default: 0 ) -bed [bed file] Only consider positions in the bed file (Default: not on/not used ) -mask [bed file] Mask these positions in the bed file (Default: not on/not used ) -paired Allow paired reads (Default: not on/not used ) You can specify either one of the two: -single Use the deamination profile of a single strand library (Default: not on/not used) -double Use the deamination profile of a double strand library (Default: not on/not used) or specify this option: -both Report both C->T and G->A regardless of stand (Default: not on/not used) Output options: -5p [output file] Output profile for the 5' end (Default: /dev/stdout) -3p [output file] Output profile for the 3' end (Default: /dev/stdout) -dp Output in damage-patterns format (Default: not on/not used) -h More human readible output (Default: not on/not used) -q Do not print why reads are skipped (Default: not on/not used) []$ diffprof Usage diffprof <options> [prof file 1] [prof file 2] This program reads 2 .prof files produced by bam2prof and outputs the difference on STDOUT Other options: -abs Use absolute value (Default: 0) |