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.
- It only works for human genome which have 22 + X + Y chromesomes and MT.
- It only works for GT type of vcf.
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.
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
.
You can run vcfmerger without arguments to see help.