PopPoly, version 2.2, Ehsan Motazedi (ehsan.motazedi@gmail.com), last modified: Aug 15 2018
PopPoly (executable main.py) is a tool for haplotype estimation in polyploid F1 populations. PopPoly uses all of the population reads to estimate the maximum likelihood parental haplotypes, from which offspring haplotypes are selected using the MEC criterion.
The algorithm is based on a Bayesian framework to choose the most likely parental haplotypes using sequence reads, and applies Mendelian inheritance rules, assuming no recombination between the SNPs, to weight each candidate phasing for the parents and to later choose the offspring phasings from the parental haplotypes. It can also re-assign the dosages for all or missing SNPs using the Mendelian rules and sequence reads. The name of the parents in the F1 population must be provided as input parameter, with the possibility to specify just one parent in self-fertilizing populations. Otherwise the first two samples registered in the BAM header will be counted as parents. Also, the VCF file must contain only SNPs, that is to say no complex variants and indels. This can be achieved by running the break_vcf.sh script on the original VCF file.
PopPoly is written in Python and is compatible with both Python 2 and Python 3. There is also a perl wrapper available PopPoly_wrapped.pl to directly use input files that contain multiple contigs, in which case one has to specify the name of the desired contig for haplotyping through the wrapper option. The wrapper also allows to filter SNPs based upon their genotype missing rate in the population and can be run using the original VCF file as it calls break_vcf.sh internally (see PopPoly_wrapped.pl -h).
It is also possible to exclude some of the individuals from analysis, for example if several replicates of the same sample are present under different names and one wishes to use only one of them. The space separated names of the to be excluded individuals must be stord in the shell environment in a variable called exclude before running PopPoly, as follows:
export exclude="sample_1_replciate_2 sample_2_replicate_1 sample_3_replicate_2 sample_3_replicate_3"
Note that PopPoly relies on pysam and numpy, which must have been properly installed before PopPoly is called. Some users have reported problems with numpy undefined symbol, a discussion of which can be found [here] (https://stackoverflow.com/questions/36190757/numpy-undefined-symbol-pyfpe-jbuf).
For the input parameters, see the help of the software:
./main.py --help, -h
Example:
./main.py bamfile vcffile output_dirname --kappa 0.85 -a 0.8 --rho 0.2 --impute
To cite PopPoly, please refer to Family-based haplotype estimation and allele dosage correction for polyploids using short sequence reads, Ehsan Motazedi, Chris Maliepaard, Richard Finkers and Dick de Ridder, 2018, bioRxiv 318196; doi: https://doi.org/10.1101/318196
The software is available at gitlab, Wageningen UR: