Thomas Sunghoon Huh
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Activity overview
Latest activity by Thomas Sunghoon Huh-
Thomas Sunghoon Huh commented,
Sorry for the late reply. I was almost buried in the pile of documents recent days. Command line I used : gatk --java-options '-Xmx32g' Mutect2 --tmp-dir gatk_tmp -L /panel/dev/C_WES_hg38.sort.bed ...
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Thomas Sunghoon Huh created a post,
FilterMutectCalls complains about the --ob-prior file's result
Hi team, While I'm using the Mutect2, the FilterMutectCalls failed to execute with the error message descripted below. It is strange that the f1r2 orientation bias was calculated together with the ...
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Thomas Sunghoon Huh created a post,
Mutect2 VCF sample order in tumor normal paired call
Hi team I'm calling somatic variants from FFPE and PBMC paired samples. I'm wondering is there any sample order preferences in Mutect2 output (such as alphenumeric order). The tumor/normal order is...
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Thomas Sunghoon Huh commented,
Genevieve Brandt (she/her) So the local realignment performs automatically when the Mutect2 engine is invoked. And after local realignment, some reads are aligned different way compared to the orig...
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Thomas Sunghoon Huh commented,
Hi Genevieve Brandt (she/her) Do you mean that there is some possibility that those alternate alleles were possibly arose from the re-alignment? Does it mean that I need to perform realignment befo...
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Thomas Sunghoon Huh commented,
Hi Genevieve Brandt (she/her) Sorry for my late reply. It took time for reading the articles you shared. I read the articles and the pdf file that you have shared. Also I found this link (https://g...
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Thomas Sunghoon Huh commented,
Hi Genevieve Brandt, After I read the article you shared, I have one question. Why do we need reference graph to be constructed first not just by starting from mapped reads?If the engine re-aligns ...
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Thomas Sunghoon Huh created a post,
Mutect2 output haplotype BAM has more alternate allele than original BAM
AnsweredIf not an error, choose a category for your question(REQUIRED): (c)a)How do I (......)? b) What does (......) mean? c) Why do I see (......)? d) Where do I find (......)? e) Will (......) be in fut...