v1.2.8

View

Now you can view vcf files from terminal:

• arrow down -> next line
• arrow up -> previous line
• arrow right -> right
• arrow left -> left
• ENTER -> next page
• SPACE -> enter line number
• ESC -> quit

vcf_tools -view -vcf ./data/merge/test_merged.vcf

Zarr format

You can convert .vcf file to zarr (.vcz) format:

vcf_tools -save_vcf_as_zarr \
    -vcf ./data/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \
    -o ./data/test.vcz \
    -show_progress \
    -num_cpu 7

• MatrixTableConsumer().save_vcf_as_zarr convert .vcf file to zarr (.vcz) format
• MatrixTableConsumer().load_zarr_data loads zarr data
• MatrixTableConsumer().sample_qc_analysis sample quality analysis

v1.2.7

Now it is possible to merge multiple vcf files:

vcf_tools -merge \
    --file_with_vcfs ./data/vcfs.txt \
    -o ./data/test_merged.vcf

Where vcfs.txt is:

./data/merge/test1.vcf
./data/merge/test2.vcf

v1.2.5

You can filter .vcf and .vcf.gz files (&& and || operators is available):

python matrix_table_consumer/vcf_tools.py -filter \
    -o ./data/test_1.vcf \
    -vcf ./data/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \
    -i "(QUAL>=90 && AF>=0.00001) || AF>=0.001" \
    -gzip \
    -num_cpu 7

v1.2.2

MatrixTableConsumer v1.2.2

You can look at the benchmarks.md file, which contains benchmark of my program and bcftools

Now you can filter .vcf files (currently only the && operator is available):

python matrix_table_consumer/vcf_tools.py -filter \
    -o ./data/test_1.vcf \
    -vcf ./data/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \
    -i "QUAL>=90 && AF>=0.00001" \
    -gzip \
    -num_cpu 7

You may donate to matrix_table_consumer project:

• Ethereum: 0xE2e2D675a3843f4ED211BB93847ad18b0A6fe7c6

v1.1.0

MatrixTableConsumer v1.1.0

To run tests, use:

pytest

You may donate to matrix_table_consumer project:

• Ethereum: 0xE2e2D675a3843f4ED211BB93847ad18b0A6fe7c6

v1.0.0

MatrixTableConsumer v1.1.0

To install this package run (you need to have Go):

pip install build
pip install .

To compile Go modules with C types to work with Python run:

export CGO_ENABLED=1

go build -o functions.so -buildmode=c-shared functions/functions.go

We have a class MatrixTableConsumer, which performs operations on Hail matrix table:

• MatrixTableConsumer().prepare_metadata_for_saving saves matrix table metadata to json format

• MatrixTableConsumer().prepare_metadata_for_loading loads table metadata

• MatrixTableConsumer().collect gives num_rows rows from vcf file (it can also open vcf.gz)

• MatrixTableConsumer().collect_all collects all table rows from vcf file (it can also open vcf.gz)

• MatrixTableConsumer().convert_rows_to_hail converts rows to Matrix Table format

• MatrixTableConsumer().create_hail_table collects table from rows

• MatrixTableConsumer().combine_hail_matrix_table_and_table combines MatrixTable and Table

• MatrixTableConsumer().count returns number of rows in the vcf file

You may donate to matrix_table_consumer project:

• Ethereum: 0xE2e2D675a3843f4ED211BB93847ad18b0A6fe7c6