tc
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Latest activity by tc-
tc commented,
It seems not to be resolved — still waiting for the GATK team. I switched to oncotator instead since I used GRCh37 reference genome for that dataset, and it worked well!
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tc commented,
Hi Genevieve, Hope everything is going well with you. I am writing to follow up with you on this issue. Wondering if there would be any update. I believe your development team would be super busy. ...
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tc commented,
Hi Genevieve, I really appreciate all your generous supports. Basically, I have several tumor samples with unmatched normal samples. I am following GATK's somatic CNV calling workflow.The data I h...
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tc commented,
Hi Genevieve, Sorry for another message. I also tried to convert the contig names in b37 to those in hg19 (by simply adding chr, so 1 will be converted to chr1). After that, I re-ran FuncotateSegme...
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tc commented,
Hi Genevieve, Thank you for looking into my issue. Yes, the reference genome I used is b37, where contigs are 1,2,3,..... When running FunctateSegments, the following messages pop up: 12:37:55.542 ...
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tc created a post,
java.lang.IllegalArgumentException: Invalid interval in FuncotateSegments
Hi, I tried to annotated a called segment file after following the somatic CNV detection workflow of GATK: gatk --java-options "-Xmx10g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID" FuncotateSegments ...