Remove variants in VCF with the same call in all but the reference

Question

[goatsrunfaster]

I have a VCF file with individuals mapped to a reference. In many cases, all of the individuals have the same allele call (although it is different from the reference). What I want to do is filter this VCF so I only have allele calls that are variable within my samples. Is there a straightforward way to do this? In the example below I want to keep Chromosome 3416, but get rid of all others:

Chromosome  72  .   T   G   .   PASS    .   GT  1   1   1   1   1
Chromosome  1993    .   T   C   .   PASS    .   GT  1   1   1   1   1
Chromosome  3416    .   C   T   .   PASS    .   GT  0   0   1   1   0
Chromosome  4190    .   G   T   .   PASS    .   GT  1   1   1   1   1

Answer 1

[guillaume.rbt]

You can achieve that with SnpSift filter : http://snpeff.sourceforge.net/SnpSift.html

For example if you want to filter out all positions where all your 5 samples are variants :

cat variants.vcf | java -jar SnpSift.jar filter "!(isVariant( GEN[0] ) & isVariant( GEN[1] ) & isVariant( GEN[2] ) & isVariant( GEN[3] ) & isVariant( GEN[4] ) )" > filtered.vcf

Answer 2

[Pierre Lindenbaum]

bcftools view -i 'AC!=5' input.Vcf