diff --git a/README.md b/README.md index 0b4032d..2907ee2 100644 --- a/README.md +++ b/README.md @@ -6,14 +6,14 @@ This project provides a Java implementation to convert your 23andMe genotype dat Your personal genome can be downloaded from [here](https://www.23andme.com/you/download). After entering your secure answer, the complete dataset can be downloaded at once. ## Generate VCF files -The VCF files are generated by combining information from your 23andMe data with the human reference file. This project uses [HTSJDK](https://github.com/samtools/htsjdk) for many tasks. +The VCF files are generated by combining information from your 23andMe data (.zip or .txt) with the human reference file. This project uses [HTSJDK](https://github.com/samtools/htsjdk) for many tasks. ```bash git clone https://github.com/seppinho/23andme-tools.git cd 23andme-tools mvn install -java -jar vcf-tools-0.1.jar vcf-generator --in --ref ---out [--exclude --ref +--out [--exclude ] [--split false] ``` The current version of the 23andMe genotyping chip v4 (> Nov 2013) is based on the GRCh37 reference (aka g1k, v37) ```human_g1k_v37.fasta```. By setting ```--ref v37``` it will be downloaded automatically. @@ -24,10 +24,10 @@ The current version of the 23andMe genotyping chip v4 (> Nov 2013) is based on t This command downloads the fasta reference and writes each chromosome (chr1-22,X,Y,MT) to a seperate vcf.gz file: ```bash -java -jar vcf-tools-0.1.jar vcf-generator --in /path/to/23andMe-genome.txt +java -jar vcf-tools-0.1.jar vcf-generator --in /path/to/genome --ref v37 --out /path/to/vcfDir ``` -Add ```--split false``` to write one VCF file. The chromosome MT file can be used with HaploGrep2. + The chromosome MT file can be then used with e.g. HaploGrep2. Add ```--split false``` to write one VCF file. ### Generating VCFs for Michigan Imputation Server The Imputation Server accepts vcf.gz files split by chromosome, which can be created with the following command: