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Description:

PopCon 1.0.5

Pop-Con: a tool to visualize genotype profiles on Site Frequency Spectrum
INTRODUCTION
Pop-Con is a tool designed to visualize genotype profiles of a Site Frequency Spectrum (SFS) from a Variant Calling Format (VCF) file [1] for SNP and indel variant.
We define a genotype profile as the list of genotypes for all individuals at a given site.
For example, "0/1,1/1,0/1,0/1" is the genotype profile corresponding to the VCF line below:
Dst_b1v03_scaf00008 54329 . G A 1970.68 PASS AC=6;AF=0.500;AN=12;BaseQRankSum=-6.140e-01;ClippingRankSum=0.00;DP=144;ExcessHet=4.8280;FS=6.723;MLEAC=5;MLEAF=0.417;MQ=60.00;MQRankSum=0.00;QD=15.28;ReadPosRankSum=-8.460e-01;SOR=0.440 GT:AD:DP:GQ:PL 0/1:16,22:38:99:558,0,409 1/1:1,11:12:3:309,3,0 0/1:26,28:54:99:750,0,617 0/1:8,11:19:99:286,0,203

Where individuals 1, 3 and 4 are heterozygote ("0/1") and individual 3 is homozygote for the alternative allele ("1/1") for this site.
Pop-Con takes as input a VCF file and uses the cyvcf2 python package [2] to read and parse the VCF file
To be readable and parsable by cyvcf2 the VCf file has to be compressed and indexed with one of the 2 following command lines:
bgzip input_vcf_file.vcf
tabix -p input_vcf_file.vcf.gz

OR
bcftools view input_vcf_file.vcf -Oz -o input_vcf_file.vcf.gz
bcftools index input_vcf_file.vcf.gz

Pop-Con has been developped on VCF files produced with GATK [3] and read2snp [4] variant callers. Variant caller used to produced VCF file has to be given with option --tool (GATK is the default variant caller).
--read and --marft filtering options can be used to test different set of genotype filtering:

--read option take as input a list of read coverage threshold. Genotype with read coverage lower than threshold will be tagged lowCov
--marft option take as input a list of minor allele read frequency threshold. Genotype with minor allele read frequency lower than threshold will be tagged lowMARF

For each filtering combination ("read coverage" + "minor allele read frequency"), Pop-Con plots 2 figures (for SNP and indel):

with sites where all individuals are genotyped and passed read coverage and minor allele read frequency filtering.
with all sites where at least 1 individual is genotyped and passed read coverage and minor allele read frequency filtering.

For figure 1, two plots are produced:

an upper plot representing the observed proportion of the X most represented genotype profiles for each SFS pic (X is set with the -max/--max_profiles option)
a lower plot representing for each pic the expected proportion of genotype profile under the Hardy-Weinberg equilibrium. Genotype profiles are colored in red if observed genotype profile is Y times upper Hardy-Weinberg expectation, blue if Y times lower and white if at equilibrum (between Y times upper and Y times lower). Where Y is set with the option -fold/--hwe_fold_change

For figure 2, only SFS plot with observed genotype profiles proportion is produced. This plot can be used to detect abnormal porpotion of low read coverage, low minor allele read frequency or ungenotyped individuals but display is not satisfying for now...
Pop-Con is supported on Linux with python2 (version==2.7) and python3 (versions>=3.4) and surely supported on Macintosh and Windows with the pypi python packages manager but not tested.
INSTALLATION
Source from GitHub
This assumes that you have the python modules cyvcf2, numpy and matplotlib installed (cf requirements.txt).
git clone https://github.com/YoannAnselmetti/Pop-Con.git
cd Pop-Con
python ./Pop-Con

Using pip (recommended)
sudo pip install Pop-Con

Manual installation
In the Pop-Con folder where "setup.py" is located, run:
sudo python setup.py install

If you encountered problem during the installation of cyvcf2 or get this following error message when executing Pop-Con:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.6/site-packages/cyvcf2/__init__.py", line 1, in <module>
from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: /usr/local/lib/python3.6/site-packages/cyvcf2/cyvcf2.cpython-36m-x86_64-linux-gnu.so: undefined symbol: EVP_sha1

You have to install it manually from the source:
https://github.com/brentp/cyvcf2
USAGE
usage: Pop-Con [-h] -i VCF_FILE [-t VARIANT_CALLER]
[-r READ_COVERAGE_THRESHOLD [READ_COVERAGE_THRESHOLD ...]]
[-m MARFT [MARFT ...]] [-f VARIANT_CALLER_FILTERING]
[-fmono MONOMORPH_FILTERING] [-p PREFIX] [-v VERBOSE]
[-o OUTPUT_DIR] [-hf WRITE_HETEROZYGOSITY_FILE] [-sep SEP]
[-max MAX_PROFILES] [-fold HWE_FOLD_CHANGE]

Pop-Con - A tool for Population genomic Conflicts detection.

optional arguments:
-h, --help show this help message and exit
-i VCF_FILE, --input_file VCF_FILE
Variant Calling Format file containing variant calling
data.
-t VARIANT_CALLER, --tool VARIANT_CALLER
Variant calling tool used to call variant. Values:
"read2snp" or "GATK". (Default: "GATK")
-r READ_COVERAGE_THRESHOLD [READ_COVERAGE_THRESHOLD ...], --read READ_COVERAGE_THRESHOLD [READ_COVERAGE_THRESHOLD ...]
List of read coverage threshold filtering for each
genotype. Values range: [0,infinity[. (Default: 0)
-m MARFT [MARFT ...], --marft MARFT [MARFT ...]
List of Minor Allele Read Frequency (MARF) threshold
for heterozygous genotypes filtering. Values range:
[0.0,0.5]. (Default: 0.0)
-f VARIANT_CALLER_FILTERING, --variant_caller_filtering VARIANT_CALLER_FILTERING
Boolean to set if variant caller filtering is consider
or not. (if "True", sites with TAG column are not
empty are filtered out from analysis). (Default: True)
-fmono MONOMORPH_FILTERING, --monomorph_filtering MONOMORPH_FILTERING
Boolean to filter out monomorph sites. ("True":
monomorph sites are filtered out from analysis. Reduce
drastically the execution time!!!). (Default: True)
-p PREFIX, --prefix PREFIX
Experiment name (used as prefix for output files).
(Default: "exp1")
-v VERBOSE, --verbose VERBOSE
Verbose intensity. (Default: 1)
-o OUTPUT_DIR, --output OUTPUT_DIR
Output directory path. (Default: ./)
-hf WRITE_HETEROZYGOSITY_FILE, --heterozygosity_file WRITE_HETEROZYGOSITY_FILE
Boolean to set if the heterozygosity files
(summarizing VCF file for each combination of read
coverage and MARF filtering) have to be written or
not. File used by script
"scripts/plot_SFS_geneotype_profiles.py" to plot SFS
without re-parsing VCF file. (Default: True)
-sep SEP, --separator SEP
Separator used in genotype profiles. (Default: ",")
-max MAX_PROFILES, --max_profiles MAX_PROFILES
Maximum number of genotype profiles displayed in SFS
plot. (Default: 10)
-fold HWE_FOLD_CHANGE, --hwe_fold_change HWE_FOLD_CHANGE
Fold change value to define when an observed genotype
profile proportion is in excess/deficit compare to the
expected value under Hardy-Weinberg Equilibrium.
(Default: 2.0)

Source code and manual: http://github.com/YoannAnselmetti/Pop-Con

EXAMPLE
Below, the minimal command line to run Pop-Con:
python Pop-Con -i input_vcf_file.vcf.gz

If the VCF file contains SNP and indel variants, Pop-Con will create two directories "SNP/" and "indel/" in current directory.
Below, an example on VCF file present in directory "example/data/Lineus_longissimus/":
python Pop-Con -i example/data/Lineus_longissimus/Lineus_longissimus_read10_par0.vcf.gz -p Lineus_longissimus -o example/results/Lineus_longissimus/ -t read2snp -fmono True -max 20

Below the architecture of the output directory "example/results/Lineus_longissimus/" produced by Pop-Con with command line above:
example/results/Lineus_longissimus/
└── SNP
├── heterozygosity
│ └── heterozygosity_allFilter_Lineus_longissimus.tab
└── MARFt0.0
├── heterozygosity
│ └── read0
│ ├── genotype_profiles_distrib_read0_Lineus_longissimus_SNP_MARFt0.0.tab
│ ├── genotype_profiles_per_altNb_read0_Lineus_longissimus_SNP_MARFt0.0_max20_with_all_positions.tab
│ ├── genotype_profiles_per_altNb_read0_Lineus_longissimus_SNP_MARFt0.0_max20_with_positions_with_all_individuals_genotyped.tab
│ └── heterozygosity_read0_Lineus_longissimus_SNP_MARFt0.0.tab
└── SFS_profiles
└── read0
├── SFSplot_genotypes_profiles_read0_Lineus_longissimus_SNP_MARFt0.0_max20_all_positions.pdf
└── SFSplot_genotypes_profiles_read0_Lineus_longissimus_SNP_MARFt0.0_max20.pdf

The 2 SFS plot with genotype profiles produced:
For sites where all individuals are genotyped and passed read coverage + minor allele read frequency filtering
File: "SFSplot_genotypes_profiles_read0_Lineus_longissimus_SNP_MARFt0.0_max20.pdf"

For sites where at least 1 individual is genotyped and passed read coverage + minor allele read frequency filtering
File: "SFSplot_genotypes_profiles_read0_Lineus_longissimus_SNP_MARFt0.0_max20_all_positions.pdf"

BIBLIOGRAPHY
[1] Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
[2] Pedersen, B. S. & Quinlan, A. R. cyvcf2: fast, flexible variant analysis with Python. Bioinformatics 33, 1867–1869 (2017).
[3] McKenna, A. et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
[4] Gayral, P. et al. Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate–Invertebrate Gap. PLOS Genetics 9, e1003457 (2013).
TROUBLESHOOTING
You get the following error message, when you forgot to set the option --tool read2snp.
Traceback (most recent call last):
File "./Pop-Con", line 404, in <module>
individuals_number,dict_SNP_genotypes,dict_indel_genotypes=read_VCF_file(vcf_file,prefix,OUTPUT,list_read_coverage_threshold,list_MARFt,monomorph_filtering,sep,verbose)
File "./Pop-Con", line 127, in read_VCF_file
dict_SNP_genotypes,dict_SNP_SFS_allPos,dict_SNP_SFS_allIndGT,dict_SNP_hetero,dict_FIS=heterozygosity.store_polymorphism(variant,list_Individuals,dict_SNP_genotypes,dict_SNP_SFS_allPos,dict_SNP_SFS_allIndGT,dict_SNP_hetero,dict_FIS,OUTPUT,'SNP',prefix,list_read_coverage_threshold,list_MARFt,False,variant_caller,write_heterozygosity_file,sep,verbose)
File "/home/yanselmetti/Bureau/Pop-Con/popcon/heterozygosity.py", line 365, in store_polymorphism
variant_size,x,y,z,listInd,dict_SFS_allPos,dict_SFS_allIndGT=store_SFS(variant,dict_SFS_allPos,dict_SFS_allIndGT,read_coverage_threshold,MARFt,bool_INDEL,variant_caller,verbose)
File "/home/yanselmetti/Bureau/Pop-Con/popcon/heterozygosity.py", line 212, in store_SFS
alt,x,y,z,listInd=get_polymorphism_GATK(variant,read_coverage_threshold,MARFt)
File "/home/yanselmetti/Bureau/Pop-Con/popcon/heterozygosity.py", line 54, in get_polymorphism_GATK
str_coverage=str(variant).split()[x].split(":")[1]
IndexError: list index out of range

This error can also arise if you used an other variant caller tool than GATK or read2snp as Pop-Con was only tested on VCF files produced by those. If you encountered such problem can you please write an issue, I'll try to shortly produce a new module to parse the VCF produced by the variant caller you used.
MISCELLANEOUS
For R lovers, there is an extra script ("scripts/SFS_genotypes_profiles_plot.R") to plot SFS with genotype profiles from file.
Example:
Rscript ./scripts/SFS_genotypes_profiles_plot.R example/results/Lineus_longissimus/SNP/MARFt0.0/heterozygosity/read0/genotype_profiles_per_altNb_read0_Lineus_longissimus_SNP_MARFt0.0_max20_with_positions_with_all_individuals_genotyped.tab 20 6 Lineus_longissimus example/results/Lineus_longissimus/SNP/MARFt0.0/SFS_profiles/read0/SFSplot_genotypes_profiles_read0_Lineus_longissimus_SNP_MARFt0.0_max20_with_Rscript.pdf 0

This script only plot SFS with observed porportion of genotype profiles and the one with comparison to the expected values under the Hardy-Weinberg equilibrium:

Contact
Yoann Anselmetti : yoann.anselmetti@umontpellier.fr