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dbSNP_RS seems to not be annotated with Oncotator 1.9.1 (Broad Internal) #357

Open brendanreardon opened 7 years ago

brendanreardon commented 7 years ago

Oncotator 1.9 seems to not be annotating dbSNP annotations (dbSNP_RS), leaving all elements blank in this column. This was tested both on Firehose (Oncotator_v1 v74) and command line implementation of Oncotator on the Broad internal VMs (specifically, cga02). Multiple datasource directories were used and this was observed as a repeatable behavior (xchip/cga/reference/annotation/db/oncotator_v1_ds_June112014/, /xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016 were specifically tested). This is also observed with multiple samples and from both the TCGAMAF input format as well as MAFLITE format.

We talked about this in person some time ago, but I wanted to cover my bases more before formally reporting it.

Below is an example usage statement...

oncotator -v --input_format=TCGAMAF --output_format=TCGAMAF --db-dir=/xchip/cga/reference/annotation/db/oncotator_v1_ds_April052016/ --default_config /xchip/cga/reference/annotation/db/tcgaMAFManualOverrides2.4.config --tx-mode=EFFECT --prepend -c /crsp/fh-data/reference/hg19/capture-pipeline/v1.2/tx_exact_uniprot_matches.txt HCC1143_oncotator-v1.9/HCC1143_TP_NT_HCC1143T_HCC1143N.oxoG3.maf.annotated.retry HCC1143_oncotator-v1.9/HCC1143_TP_NT_HCC1143T_HCC1143N.oxoG3.maf.annotated hg19

I'm happy to help or provide more information!

sozerberk commented 7 years ago

Is there any development on this issue? dbSNP_RS annotation definitely doesn't work.