TMB
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Activity overview
Latest activity by TMB-
TMB commented,
Thank you so much for your comment. Do you have any updates on this topic? Funcotator appears to give RefSeq ID to annotate variants but it lacks version numbers ( .x) The funcotator resources ve...
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TMB created a post,
Refseq accession number and version number in Funcotator
AnsweredI used Funcotator to annotate my VCF (somatic variant calling) and worked great. Now I have to find the correct RefSeq number and version number of the reference sequence used to annotate variants...
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TMB commented,
Thank you so much. This is very helpful. TMB
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TMB created a post,
Funcotator gnomAD MAF columns
AnsweredHi I used Funcotator to annotate VCF (somatic variant calling). I am tying to filter out variants based on MAF and would like to use a female population (inclusive for all ancestries). I have use...
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TMB commented,
Hi Genevieve, Thank you for your response. I did notice there is an GC error as follows: Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded I used "-Xmx75G" instead...
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TMB commented,
Got it. That's what I did with 4.0.9.0 and worked well. Thank you so much for answering questions! Your help is much appreciated.
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TMB commented,
Just to clarify. Do I have to say "-tumor-sample" instead of "-normal"? Or either way works fine? For 4.1.9.0, I used the following script: gatk --java-options "-Xmx6G" Mutect2 -R $REF \ -I ...
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TMB commented,
Hi David, Thank you so much for your inputs. I tried the Mutect2 version 4.1.9.0 which seems to avoid this problem. Do you agree? Do I still specify anything for version 4.1.9.0 to get this righ...
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TMB created a post,
Mutect2 failing to produce F1R2.tar.gz files on TCGA bam (tumor-normal pairs)
AnsweredIf you are seeing an error, please provide(REQUIRED) : a) GATK version used: 4.1.9.0b) Exact command used: gatk --java-options "-Xmx6G" Mutect2 -R $REF -I ${BAM_DIR}/${BN}_NORMAL_DNA.fixed.bam -I...
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TMB commented,
Hi David. My command lines for Mutec2 and FilterMutectCalls are as follows: Mutect2 gatk --java-options "-Xmx6G" Mutect2 \--reference $REF \--germline-resource $RESOURCE \--input ${SAMPLE}_Bld.b...