Annotate VCF with RepeatMasker

Question

[mufernando]

Is it possible to annotate a vcf with RepeatMasker? If so, how can I do it?

Thanks

Answer 1

[Amitm]

hi, If your motive is to see if any variant in the VCF is within repeats, then you could do something like this - 1) Get the BED format file of repeats in our organism of interest 2) Then use bedtools coverage (here) to see overlap with repeats.

This relies on availability of repeat strt end pos. in your organism of interest. For many org., you can get such BED from UCSC Table Browser like this - (Use Clade and Genome pull down menu to arrive at other organisms)

[mufernando]

thank you for your response! I'll try to do that.

[mufernando]

how can I remove SNPs close to polymorphic indels? I work with Drosophila.

[Amitm]

hi,

Do you know the locations of the polymorphic InDels? If yes then you can filter out any SNP within a desired range of distance of known poly. InDels, using bedtools subtract. I haven't worked with Drosophila so I dont know of definitive resource for polymorphic InDels. But these resources might be useful if you aren't aware of any - 1) UCSC TableBrowser enlists, under Variation & Repeats group, the Simple Repeats & Microsatellite tracks which are known to be polymorphic. 2) Transposons could very well be polymorphic too. In that case this db could be usefule: TIDAL-FLY 3) Also FlyVar