I used Oncotator (1.9.3.0) to annotate VCF file.
If I run this on command line:
oncotator -v --input_format VCF --output_format TCGAMAF --db-dir /share/apps/oncotator_v1_ds_April052016/ -d . test_oncotator_ffpe.vcf oncotator.maf hg19
There will be an error:
2017-10-17 11:43:39,572 ERROR [oncotator.output.TcgaMafOutputRenderer:333] Traceback (most recent call last):
File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 317, in renderMutations
self._add_output_annotations(m)
File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 241, in _add_output_annotations
alt_count = vals[1]
IndexError: list index out of range
2017-10-17 11:43:39,572 ERROR [oncotator.output.TcgaMafOutputRenderer:334] Error at mutation 0 ['1', '11166639', '11166639', 'T', 'A']:
2017-10-17 11:43:39,572 ERROR [oncotator.output.TcgaMafOutputRenderer:335] Incomplete: rendered 0 mutations.
Traceback (most recent call last):
File "/share/apps/oncotator/bin/oncotator", line 11, in <module>
load_entry_point('Oncotator==1.9.3.0', 'console_scripts', 'oncotator')()
File "build/bdist.linux-x86_64/egg/oncotator/Oncotator.py", line 309, in main
File "build/bdist.linux-x86_64/egg/oncotator/Annotator.py", line 437, in annotate
File "build/bdist.linux-x86_64/egg/oncotator/output/TcgaMafOutputRenderer.py", line 337, in renderMutations
IndexError: list index out of range
if I run this on command line:
oncotator -v --input_format VCF --output_format VCF --db-dir /share/apps/oncotator_v1_ds_April052016/ -d . test_oncotator_ffpe.vcf oncotator.maf hg19
There will not be an error,this VCF is produced by VARSCAN 2.3.4,fileformat=VCF4.1,normalized by bcftools
And if I run this on command line:
oncotator -v --input_format VCF --output_format TCGAMAF --db-dir /share/apps/oncotator_v1_ds_April052016/ -d . test_oncotator_wes.vcf oncotator.maf hg19
There will not be an error,this VCF is produced by GATK 3.8,fileformat=VCF4.2,normalized by bcftools