I am working in the research env of GEL and I am carrying out some annotation. The fact that working in this RE and I am new doing annotation are giving me some trouble I would like to ask here.
I want to use VEP and LOFTEE and I am following this tutorial.
The code I am using is pretty much the same that suggested in that tutorial
vep\
--input_file /PATH/machine_learning/Manuel/LOEUF_tool/Data_output/tmp/filtered SNPS.vcf\
--format vcf\
--offline\
-- cache\
-- cache version 98\
--assembly GRCH38\
--dir_ cache /resources/data/vep.caches/from.pegasus/98/.vep\
--verbose\
--no_stats
--fasta /public data resources/reference/GRCH38/GRCh38Decoy no alt. fa\
--plugin LoF,Loftee path:S{LOFTEE38}, human_ancestor_fa:${LOFTEE38HA}, gerp_bigwig:${LOFTEE38GERP}, conservation_file:${LOFTEE38SQL}\
--force overwrite\
--output_file /PATH/machine_learning/Manuel/LOEUF_tool/Data_output/tmp/VEP_SNPS_annotated.tsv
and I am getting a warning that I think it is responsible for the incomplete annotation of my results.
The warning:
And some variants annotated
Sorry for the pictures I cannot copy and paste from this HPC to the internet. And this is NOT patient data, they are fake variants I have created.
If we compare my output with the one found in the GitHub of the author, you can see that the Lof filtering is missing, which says if the variants pass all filters or not. HC refers to high-confidence LoF variants (i.e. does not fail any filters). LC denotes low-confidence, failing at least one filter, which are written to the LoF_filter field.
From Loftee:
A|ENSG00000184163|ENST00000330388|Transcript|stop_gained|648|616|206|Q/*|Cag/Tag|||-1|||HC,
UPDATE.
I have changed the version from 98 to 99. I don't get the error, but I don't get the output I want, the LoF flag.
