asoskins

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asoskins
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Imperial College, Lonfon, UK
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  • Hello, I've installed oncotator/1.5.1.0 and try to run it with python/2.7.3 on my vcf files with the following command line: oncotator -i VCF --db-dir $TMPDIR/oncotator_db -o VCF $TMPDIR/merged.vcf $TMPDIR/annotated.vcf hg19 I keep getting the foll…
  • Thank you, Geraldine. Upgrading to the new version made the trick.
  • Hi Geraldin, I run Oncotator on unprocessed Mutect VCF file and end up with the same error mesage: 2014-11-14 16:52:27,209 ERROR [oncotator.output.VcfOutputRenderer:222] Traceback (most recent call last): File "/apps/python/2.7.3/lib/python…
  • I used mutect/1.1.4 and oncotator/1.2.8.0. Postprocessing mutect VCF files included filtering with 'grep -v REJECT' and merging mutect outputs for genome chunks with GATK tool CombineVariants.
  • mutect/1.1.4 oncotator/1.2.8.0 I filter mutations with 'grep -v REJECT' and use GATK tool CombineVariants to merge mutect outputs for genome chunks.