HAPPE 0.0.1

HAP Plot in ExceL.

HAPPE

HAP Plot in ExceL.

Installing HAPPE

There easiest way to install HAPPE is to use pip3.

pip3 install HAPPE

then you should have the HAPPE command available.

HAPPE -h

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 file

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  sample1.bam

running HAPPE

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./[e-mail]

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]
  -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.[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

example

HAPPE \
-g config.ini \
-v test.vcf.gz \
-r chr7A:71669854-71670886 \
-i 1059_Inf.txt \
-c 1059.pop.color \
-F FunctionalAnnotation_v1__HCgenes_v1.0.TAB \
-D path/to/depth_data/ \
-f \
-o test
## each file of the prameter
## -g config.ini
# [software]
# bgzip=path_to/bgzip
# bcftools=path_to/bcftools
# tabix=path_to/tabix

## -i 1059_Inf.txt
## Just make sure the first column is the sample name.
# Sample_ID	... ...
# sample1   ... ...

## -c 1059.pop.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 path/to/depth_data/
##Make sure that the files *mosdepth.summary.txt and *per-base.bed.gz are in the directory for each sample in this directory.