vcf-merge

[runnerBio88]

Hi

I have several vcf files, raw and annotated.
I've used vcf-merge without any option. The output file I used it check for recurrent mutations.

I'm not able to understand (as the documentation is almost none). When vcf-merge merges vcf files is it doing it by position?

What happens if I have something like (being each line a different sample)

chr pos ref alt
1 200 A C
1 200 A T
1 200 A -
1 200 A TT

Different mutations happen in same coordinates. Are thos mutationes going to be treated as the same? I think I want to have recurrent genes and recurrent positions.

Thanks

[azneto]

You should try 'bcftools merge'

https://samtools.github.io/bcftools/bcftools-man.html#merge

By default it will merge you're samples like this:
1 200 A C,T,-,TT

But you can tweak the -m parameter in order to get different results.
Good luck

[runnerBio88]

Thanks

I did some test and as you said that is what vcf-merge does.

I've alse checked bcftools merge, but as the input paramters are almost the same I used vcf-merge.

Is it worthy to use bcftools over vcf-merg?

Thaks

[Brian Bushnell]

I've heard that bcftools is far faster than vcftools, though I've not personally used either of them...