jungmin choi
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Activity overview
Latest activity by jungmin choi-
jungmin choi created a post,
disabling NotDuplicateReadFilter in Mutect2
Can you please provide a) GATK version used 4.1.4.1b) Exact GATK commands used Mutect2c) The entire error log if applicable. I am analyzing targeted sequencing data on tumor samples where I need ...
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jungmin choi commented,
I am no longer reproducing the bamout errors. It must have been a syntax mistake on my side. Please disregard my question. Thanks!
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jungmin choi commented,
David Benjamin Thanks for confirming this. I am also getting errors when I specify -bamout parameter like below. Is this expected as well? -bamout <pair>/gatk4.1_multisample/<pair>.mutect2.<chu...
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jungmin choi commented,
David Benjamin I am a bit perplexed to see the results like below. The order of the samples is tumor1, normal, and tumor2 from the same patient. Is the tool genotyping the tumor automatically heter...
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jungmin choi commented,
David Benjamin Thank you and great to have the latest Mutect2 documentation now.
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jungmin choi created a post,
calculateContamination step with multi-tumor samples
Can you please providea) GATK version used gatk-4.1.4.1b) Exact GATK commands used gatk CalculateContamination -I getpileupsummaries.table -O calculatecontamination.table -tumor-segmentation segmen...