VCF Merger
What is vcfmerger?
Like its name, it merges multiple vcf files into one. It does things similar to vcf-merge in vcf-tools.
Although vcf-merge might do the same thing, it is considerably slow, and for big size of data, I don't even dare to try.
This tool is written in C++, and aims to merge numerous (say, 1 million) human genome vcfs togather, and to do it efficiently.
Notice
- It only works for human genome which have 22 + X + Y chromesomes and MT.
- It only works for GT type of vcf.
PBWT version
When two files have different alts at same position, it simply merge them into two lines of vcf file, for speed and simplicity. I know it violents vcf specifications, but for pbwt, it doesn't matter, as pbwt will divide multi alts into different sites.
Make and Installation
git clone https://github.com/CoREse/vcfmerger
cd vcfmerger
make
sudo make install
or you can do
make PREFIX=/some/prefix install
to indicate your own prefix(instead of the default /usr/bin).
If you want to remove the program, just
sudo make remove
or
make PREFIX=/some/prefix remove
.
Usage
You can run vcfmerger without arguments to see help.