Update README.md

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 <your-genome.txt> --ref </path/to/human_g1k_v37.fasta> 
---out <vcf-destination-folder> [--exclude <chromosomes to exclude] [--split false]
+java -jar vcf-tools-0.1.jar vcf-generator --in </path/to/genome> --ref </path/to/human_g1k_v37.fasta> 
+--out <vcf-destination-folder> [--exclude <chromosomes to 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: