Filtering SNPs on identical genotype and position

[htetre]

Hello,

Did you ever find a good tool to filter out SNPs with genotypes across your samples?

I am looking to do the same, filter sites that are invariant across samples that are in a single vcf file. It sounds easy but I haven't found a good tool to do so.

Are there any suggestions?

Thank you

[Mr. Lolium]

Hi Jessica,

Thanks for the reply.
Bedtools intersect is not what i'm looking for. Let me clarify myself...

I have a list of SNP positions and genotype data, e.g:

Scaffold | position | sample 1 | sample 2 | sample 3
1 | 100 | 0 | 1 | 2
1 | 150 | 0 | 1 | 2
1 | 175 | 0 | 1 | 1
1 | 300 | 0 | 1 | 2

The entire line at position 150 has to be removed, because that one has identical genotypes as position 100.
Position 175 should be kept, because that one has a different genotype in sample 3 compared to position 100.
Position 300 should be kept also. Alltough it has the same genotype as position 100, it is more than 100 bp forward compared to position 100.

[Jessica_L]

have you looked at a tool like bedIntersect on bedtools? Or are you trying to filter out only a particular allele for a given variant? For example, if there's a SNP that can be either A, G, or T, are you trying to remove that variant from your vcf altogether or do you just want to remove anything that's been called as an A?

[Mr. Lolium]

Hello everyone,

I'm looking for software that is able to filter out SNPs which:
- have an identical genotype across all samples
- and are within a certain range (f.e. 100 bp)
Preferably it should work on VCF files, but other suggestions are fine too.

It shouldn’t be too hard to script this myself, but it would be great if someone knows an available tool for this.
Thanks!