genoFreq

Summarize and visualize the genotypes categories per sample in a VCF file.

genoFreq is designed to process very large VCF files (Terabytes) with high speed & very low memory consumption.

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Build

git clone --recursive https://github.com/mr-eyes/genoFreq.git
mkdir -p genoFreq/build && cd genoFreq/build/
cmake ..
make

Install Python dependencies

python -m pip install -r requirements.txt

1- Generate genotype frequencies

Run

./genoFreq <file.vcf/file.vcf.gz> <output_dir> <optional: max_haplotype_number, default=6>

Output Sample "TSV"

sample	./.	0/0	0/1	0/2	0/3	0/4	0/5	0/6	1/0	1/1	1/2	1/3	1/4	1/5	1/6	2/0	2/1	2/2	2/3	2/4	2/5	2/6	3/0	3/1	3/2	3/3	3/4	3/5	3/6	4/0	4/1	4/2	4/3	4/4	4/5	4/6	5/0	5/1	5/2	5/3	5/4	5/5	5/6	6/0
SAMPLE1	1443	6168	98	3	0	0	0	0	0	18	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
SAMPLE2	3361	4259	58	2	0	0	0	0	0	49	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
SAMPLE3	2856	4740	98	1	0	0	0	0	0	35	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0

2- Combine multiple frequencies TSVs (Optional)

Run

python scripts/combine_freqs.py <file1.tsv> <file2.tsv> ...

Or

python scripts/combine_freqs.py ./*tsv

3- Simplify genoTypes to categories

Run

python scripts/simplify.py <genpFreq.tsv>

Output Sample "TSV"

sample	ungenotyped	homo_WT	homo_MT	hetero	comp_het
SAMPLE1	1443	6168	18	101	0
SAMPLE2	3361	4259	50	60	0
SAMPLE3	2856	4740	35	99	0

4- Merge samples meta information with genotypes frequencies

Meta information file sample (flixble for changes)

SampleID	Breed	Sex	Coverage
SAMPLE1	Breed1	M	9.62
SAMPLE2	Breed2	M	13.69
SAMPLE3	Breed3	M	13.69

Run

python scripts/merge.py <metaInfo.tsv> <genoFreq.tsv>

Sample

SampleID	Breed	Sex	Coverage	ungenotyped	homo_WT	homo_MT	hetero	comp_het
SAMPLE1	Breed1	M	9.62	1443	6168	18	101	0
SAMPLE2	Breed2	M	13.69	3361	4259	50	60	0
SAMPLE3	Breed3	M	13.69	2856	4740	35	99	0

5- Visualization

Run

python scripts/plot.py <merged_file.tsv> <x_axis> <y_axis>

Sample