test_data.txt

# Dataset for testing VarMatch:
http://www.bx.psu.edu/medvedev_lab/varmatch_test_data.tar.gz

It contains three files:
1. ref.fa
ref.fa is genome sequence of chromosome 22 of GRCh37
2. baseline.vcf
baseline.vcf is variant calling result on chromosome 22 by Freebayes.
3. query.vcf
query.vcf is variant calling result on chromosome 22 by GATK.   

You can use the following command to download test data set
> wget http://www.bx.psu.edu/medvedev_lab/varmatch_test_data.tar.gz

For Mac OS X users, if you do not have wget installed, using the following command to download test data set:
> curl -O http://www.bx.psu.edu/medvedev_lab/varmatch_test_data.tar.gz

After downloading, use the following command to test VarMatch on it:
> tar -xzvf varmatch_test_data.tar.gz
> cd varmatch_test_data
> VarMatch_Directory/varmatch -g ref.fa -b baseline.fa -q query.fa -o output -f

VarMatch_Directory is the path of VarMatch

varmatch is a python script, which calls the core executive program: VarMatch_Directory/src/vm-core