Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Question about unknown in oncotator results
Dear Oncotator developers,
I am trying to use Oncotator to annotate MAF or VCF files. According to instruction in this forum, I tried to run with test data "Patient0.snp.maf.txt", then Oncotator provides only "UNKNOWN" information from Oncotator results.
Here is my command line,
oncotator -v --db-dir /path/to/oncotator_v1_ds_Jan262015 /home/suimye/tool/oncotator-18.104.22.168/test/testdata/maflite/Patient0.snp.maf.txt exampleOutput.tsv hg19
In this result, all variants were not annotated. To evaluate this result, I put this data on Oncotator web. Then, the variants are annotated successfully.
From searching by google, I found out similar oncotator results as
Is this correct output? I suspect several warning messages observed in above logs may influence this problem such as " THERE ARE NO DATASOURCES REGISTERED" and "%s does not exist, so there will be no datasources".
If you have any suggestion, please reply me.
Thanks for development of great tools!!