intersect VCF files

[adrian]

Hi:

I like bedtools. but now GATK pipelines are spewing VCF files and I want to intersect 3 files.

For instance I have 3 VCF files F1, F2 and F3.

I want to intersect
newfile = intersect(F1, F2)

then I want to :

newsecondfile = intersect(newfile, F3)

How can I do this on VCF files. I tried vcftools, it is not handy with all the gz files and perl.

I like something a BEDtools type.

Any suggestions.

thanks
Adrian

[swbarnes2]

IntersectBed claims to accept .vcf files. I'm pretty sure I've used it myself to do just that.

What I've also done is used mpileup in samtools to take in multiple .bams files together. The downside is that it doesn't keep all the information for each sample together, but it at least give you GT, PL and GQ values for each sample. You can filter by the GT or the PL to find SNPs that are or aren't in whatever combination of samples you want.

[n00c]

There is also vcfutils vcf-isec:

http://vcftools.sourceforge.net/perl_module.html#vcf-isec

[NGSfan]

Has anyone got vcf-isec to work?

I bgzipped my vcfs and tabix'ed them..

here I try it on the same vcf:

vcf-isec -c 26530.snv.vcf.gz 26530.snv.vcf.gz

but I get:
Can't use string ("silent") as a HASH ref while "strict refs" in use at /net/home/leparc/bin/VCFtools/perl/Vcf.pm line 542.

Also, why all the trouble with bgzipping and tabix indexing... it's a lot of hassle just to do something so simple.

[dwmohr]

I've successfully run vcf-isec to compare two related individuals:

vcf-isec -n +2 -f file1.vcf.gz file2.vcf.gz > file3.vcf.gz

[GW_OK]

Have you tried vcftools?

[ekg]

There is also vcfintersect: https://github.com/ekg/vcflib#vcfintersect

It works with both BED files and VCF files, and can generate inverse intersections (allowing you to find things that are not in one file).

[Nino]

Hello,

Would anyone happen to know how to merge a set a vcf files where you have at least 20% to at most 90% of all candidates reported across all files into one new file?

Thanks,
Nino

[AdrianP]

I can also suggest R. Convert your VCF to tab files, and then intersect the positions where variants are called.