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.

[van-truong]

Based on the versions and code changes, adding this allele feature will change the schema so Andre thinks this would be best to add for 3.0.0 version

Note that this is a LOKI problem so we will need to change it there. LOKI doesn't currently have this information (or it isn't set up to retrieve it). Every time we change LOKI, we need to change Biofilter to be able to pull this information from LOKI