Estimate distances to closest gene from VCF and GFF files

Question

[elcortegano]

Hi, I am doing now some analyses that require knowledge of the distance from some variant (and invatiant) positions in VCF files to the closest genomic feature reported on a separate GFF file.

I am currently doing so by processing these two files as spreadsheets and calculating these distances with some R code, but as you can imagine this is probably suboptimal, messy, and prone to errors.

I am assuming that there is probably a package on R Bioconductor or Python that allows to generate a dataset of genomic positions taken from a VCF and distances to different genomic features in GFF files, but so far I haven't found anything.

Do you have any recommendation on how to handle this?

[ATpoint]

Check out the bedtools collection of tools and its subcommand bedtools closest.

https://github.com/arq5x/bedtools2

[elcortegano]

Perhaps I am being unlucky, but this failed for me at some <NON_REF> ALT positons. After replacing them with sed -i -e 's/<NON_REF>/./', bedtools returns a core dumped error.

[ATpoint]

Without code and data examples it is impossible to debug.