HAPPE

A tool to visualize the haplotype pattern and various information in excel. Please cite this paper when using HAPPE for your publications

Cong Feng, Xingwei Wang, Shishi Wu, Weidong Ning, Bo Song, Jianbin Yan, and Shifeng Cheng. 2022. “HAPPE: A Tool for Population Haplotype Analysis and Visualization in Editable Excel Tables.” Frontiers in Plant Science 13 (July): 927407. https://doi.org/10.3389/fpls.2022.927407.

Installing HAPPE

There easiest way to install HAPPE is to use pip3.

pip3 install HAPPE

or you can clone the project to your local directory and installing it with:

python3 setup.py install --record log.txt
#if u want to uninstall the package:
#cat log.txt | xargs rm -rf

then you should have the HAPPE command available.

$ HAPPE -h

usage: HAPPE [-h] -g CONFIG -v GZVCF [-k KEEP] [-r REGION]
                          [-s SNPLIST] -i INF -c COLOR [-I SNPINF] [-R REF]
                          [-F FUNCANN] [-f | -x | -n] [-D DEPTH] [-d DEPTHBIN]
                          -o OUTPUT

show haplotype patterns in excel file./fengcong@caas.cn

optional arguments:
  -h, --help            show this help message and exit
  -g CONFIG, --config CONFIG
                        config file.[required]
  -v GZVCF, --gzvcf GZVCF
                        gzvcf, bcftools indexed.use to annotation and get
                        ref/alt basepair.[required]
  -k KEEP, --keep KEEP  keep sample, if u wana plot a subset of
                        --gzvcf.[optional]
  -r REGION, --region REGION
                        if u wana plot a subset of --gzvcf, u can use this
                        option. if u use this option , ucant use -s
                        option[optional]
  -s SNPLIST, --snplist SNPLIST
                        snp id list(format:chr_pos). if u use this option , u
                        cant use -r option.[optional]
  -w TREEWIDTH, --treewidth TREEWIDTH
                        How many columns do you want to occupy for this tree
                        topology.(default=1000)[optional]
  -i INF, --inf INF     the information of each sample.[required]
  -c COLOR, --color COLOR
                        the color of each sample.[required]
  -I SNPINF, --snpinf SNPINF
                        more information about SNP.[optional]
  -R REF, --Ref REF     change Reference and color system.[optional]
  -F FUNCANN, --FuncAnn FUNCANN
                        functional annotation file.[optional]
  -f, --functional      only functional SNP
  -x, --coding          only coding region SNP
  -n, --noncoding       only noncoding region SNP
  -D DEPTH, --Depth DEPTH
                        depth dir for each sample.[optional]
  -d DEPTHBIN, --Depthbin DEPTHBIN
                        Depth bin size.[optional,default:50]
  -o OUTPUT, --output OUTPUT
                        output prefix

Preparing config file

[software]
bgzip=
bcftools=
tabix=

Preparing the vcf file

1. The SNP/INDEL ID must be in the format :Chromosome_position.
2. Only bi-allelic remains in vcf file.
3. Compress vcf to vcf.gz using bgzip
4. Use bcftools index to create an index for the vcf.gz file.

Preparing the depth information

if you want to integrate the depth information, you need to prepare the depth file as follows:

1. Create a directory for each sample with the name of the sample.
2. using mosdepth to calc the depth of each position for each sample.

#example
mosdepth -f ref.fa -Q 0 sample1/sample1.Q0  path/to/sample1.bam

Usage

"-g  CONFIG", required parameter, give the paths to bcftools, bgzip and tabix in the CONFIG file. 

"-v GZVCF", required parameter, input vcf file.

"-k SAMPLELIST", required parameter, list of samples to be retained, one sample per line.

"-r REGION", optional parameter, the genomic region to be displayed, format: chromosome: start-end.

"-s VARIANTLIST", optional parameter, the list of variant IDs you need to keep, using this parameter you cannot use the -r parameter.

"-w TREEWIDTH", optional parameter, the width of the tree topology.

"-i INFORMATION", optional parameter, additional sample information, the first column must be the sample ID.

"-c COLOR", optional parameter, Specify the color of each sample, the first column is the sample id and the second column is the color hex code.

"-I VARINFORMATION", optional parameter, Additional variant annotation information, such as GWAS p-value. the first colum is the variant id and each column is the annotation information with header.

"-f", optional parameter, Only the variant that changes the amino acid is retained.( Requires that the input vcf file has been annotated with SnpEff.)

"-x", optional parameter, Only the variant in the CDS region is retained.( Requires that the input vcf file has been annotated with SnpEff.)

"-n"， optional parameter, Only the variant in the non-coding region is retained.( Requires that the input vcf file has been annotated with SnpEff.)

"-D DIRECTORY"， optional parameter, This directory contains the depth information for each sample calculated using mosdepth, one directory per sample.

"-d WINDOWSIZE", optional parameter, window size for calculate normalized depth.

"-o PREFIX"， required parameter, output prefix.

example

The example data covered in the publication is in the example/ folder.

HAPPE \
-g config.ini \
-v ./data/00.annotated_vcf/SEVIR.592.SNP.ann.allele2.part.vcf.gz \
-r 5:6847970-6850236 \
-w 100 \
-d 20 \
-i ./data/02.sample_information//sample_inf.tsv \
-c ./data/02.sample_information//sample.color \
-D ./data/01.depth \
-k ./data/02.sample_information//small_example.list \
-o SEVIR_5G085400v2


## each file of the prameter
## -g config.ini
# [software]
# bgzip=path_to/bgzip
# bcftools=path_to/bcftools
# tabix=path_to/tabix

## -i ./data/02.sample_information//sample_inf.tsv
## Just make sure the first column is the sample name.
# Sample_ID	... ...
# sample1   ... ...

## -c ./data/02.sample_information//sample.color
## Just make sure the first column is the sample name and the second column is color code.
# Sample_ID	color
# sample1	FF0000
# ...       ...

## -F FunctionalAnnotation_v1__HCgenes_v1.0.TAB
## just make sure the first column is the gene name , and the forth column is the functional annotation.
# Gene_name	XXX XXX function ... ...
# gene1     XXX XXX func1    ... ...

## -D ./data/01.depth
##Make sure that the files *mosdepth.summary.txt and *per-base.bed.gz are in the directory for each sample in this directory.