bedtools intersect -f 1.0 -r -loj -a test.vcf -b ref.vcf | awk 'BEGIN{FS="\t"} $4==$14 && $5 == $15'

Bedtools intersect

Bedtools allows to control the required overlap size (-f parameter) to adjust your criteria for being a true positive. For example, if you have very long inserts a 90% overlap might be sufficient.

Anyway, look at bcftools norm to make sure that the Indels from both VCF files are represented in the same way. Unfortunately, Indels can often be represented in more than one way, particularly in low-complexity regions. I recently ran into this problem...

EDIT: Change to include REF and ALT comparison between reference and alternative.

landesfeind@bionf-local:/tmp$ cat ref.vcf
##fileformat=VCFv4.2
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    Sample1
chr1    10    .    G    GA    10    PASS    .    .    .
chr1    110    .    T    TT    10    PASS    .    .    .

landesfeind@bionf-local:/tmp$ cat test.vcf
##fileformat=VCFv4.2
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    Sample1
chr1    10    .    G    GCA    10    PASS    .    .    .
chr1    110    .    T    TT    10    PASS    .    .    .
chr1    210    .    C    CA    10    PASS    .    .    .

landesfeind@bionf-local:/tmp$ bedtools intersect -loj -a test.vcf -b ref.vcf | awk 'BEGIN{FS="\t&"} $4==$14 && $5 == $15'
chr1    110    .    T    TT    10    PASS    .    .    .    chr1    110    .    T    TT    10    PASS    .    .    .

landesfeind@bionf-local:/tmp$ bedtools intersect -loj -a test.vcf -b ref.vcf | awk 'BEGIN{FS="\t"} $4==$14 && $5 == $15' | wc -l
1

If both ref.vcf and test.vcf are in same format, you can use vcftools. In particular you may need vcf-isec

vcf-isec -n +2 ref.vcf.gz test.vcf.gz > TrueIndels.vcf

and before using vcftools, bgzip your vcf files and index with tabix.

Hi,

Is it mandatory that you have to use R or MATLAB? If not, have a look at vcftools. You can compare and filter vcf files in several different ways, and one of the most frequent usages is to identify common indels.

Cheers

The GRanges and VariantAnnotation Bioconductor packages make this pretty easy in R. Roughly, you will need to:

1. Use readVcf to read in your two VCF files.
2. Use findOverlaps(...., type="equal").

Alternatively, simply concatenate the chromosome, start, and end into a string for each variant for each VCF file. Then, use a simple intersect on the two character vectors.