Request to Query Alleles

[katiecardone26]

I think that biofilter should return reference and alternate alleles in addition to the chromosome, position, RSID, etc. This would be really useful. For example, when annotating GWAS results, I sometimes get multiple RSIDs for a particular chromosome and position. This is because there can be different types of variations at a particular position (SNP, insertion, deletion, multi-nucleotide variant). Having an allele will help to parse through these duplicates and identify what RSID matches my variant of interest. I believe these are available in the databases that LOKI pulls from.

[AndreRico]

Hi @katiecardone26. I understand that this would be an improvement. What do you think—should we implement it in the current version 2.4.3, or add it as a new feature for version 3?

[katiecardone26]

Hi @AndreRico, I think this should be implemented in the current version (2.4.3). Thanks!

[AndreRico]

Hi @katiecardone26, could you provide me the command for Biofilter and any example input data you are using, please?

[katiecardone26]

example command:

module load biofilter/2.4.3
biofilter.py \
--verbose \
--knowledge /project/ritchie00/datasets/loki/loki.db \
--position-file input_filename \
 --annotate position_label snp position gene upstream downstream \
--report-invalid-input \
--overwrite \
--prefix output_prefix \
--ucsc-build-version 38

You can make example data from any genomic data. I use a three column input with the following columns (in order): chromosome number, variant id, position. Here is a screenshot of an example input file.