Hi,
I tried out the tool bcftools query and it worked well for rather simple queries. However I am stuck at the point where I would like to only extract the first annotation of the ANN Tag in the Info field.
This is what I used for a query in Galaxy (toolshed.g2.bx.psu.edu/repos/iuc/bcftools_query/bcftools_query/1.4.0):
%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO/DP\t%INFO/UMT\t%INFO/ANN\t%INFO/ANN{0}\t%INFO/ExAC_NFE\t%INFO/AF_popmax\t%INFO/AF_nfe\t%INFO/1000g2015aug_all\t%INFO/1000g2015aug_eur\t [ %GT] \t [ %VF]\n
I am left with the following error message: Error: todo: type 7
I actually wanted not only to extract the first Annotation of the comma separated list of annotations in the ANN Tag of the INFO field, but I also wanted to further split this first annotation in its subcontents, which are separated by “|”.
Furthermore and more importantly I don’t know how to handle the problem that my gnomad annotation for genome and exome have the same INFO-Tag and bcftools only extracts one of those values (vcftotab always generated a comma separates list for alle the values available for that one INFO-TAG). Do you have any suggestions?
Thanks for the help!
All the best
Rose