sahuno
cancer genomics @Polak lab; cell-free DNA, mutational signatures, cell of origin
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Activity overview
Latest activity by sahuno-
sahuno created a post,
Somatic Hotspot mutation is filtered although evident with IGV
AnsweredHi allI can't find evidence of key mutations after Mutect2 (Tumor-Normal Mode with PoN). On the other hand, I do see the mutation with IGV and i don't know why it was filtered. For example, patie...
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sahuno created a post,
No t_depth in Funcotator MAF
AnsweredIs there a way to enable t_depth in Funcotator MAF ? however my final maf contains some info on depth "tumor_f","t_alt_count","t_ref_count","n_alt_count","n_ref_count" Thanks in advance -S GAT...
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sahuno commented,
Genevieve Brandt (she/her) No please, the samples may have been mislabeled. can I tell from the reads or something if this is likely to be tumor or normal? -S
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sahuno created a post,
For mislabelled Tumor & Normal bam files from same patient, which gatk tool approach can i use to reclassify?
Please if I have mislabelled bam files (1 should be tumor & the other germline bam file) from same patient which approach or gatk tool can i use to correctly reclassify tumor & germline bam files? ...
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sahuno commented,
Hi jejacobs23 you need the `gsutil` (google cloud command line software) to able to download google cloud objects. to install `gsutil` see here https://cloud.google.com/storage/docs/gsutil_install ...
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sahuno commented,
Samantha (she/her) Great! thanks for pointing this out! Sam
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sahuno commented,
Hi Samantha (she/her) I appreciate your time looking at the workflow and logs. You are right about conflicts in gatk docker versions in workflow and as attribute I specified. but i I don't think a...
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sahuno commented,
Hi Samantha (she/her) I've added ` GROUP_FireCloud-Support@firecloud.org ` to the current workspace and sent submission details to email. could you please confirm you have it? Kind regards SA
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sahuno created a post,
[Funcotator] java.lang.IllegalArgumentException: Unexpected value: lncRNA
Can you please provide a) GATK version used; "broadinstitute/gatk:latest" (gatk 4.1.8.1) Hello I'm running funcotator on germline samples but keeps throwing this error ` java.lang.IllegalArgumentEx...
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sahuno commented,
Genevieve Brandt (she/her) thanks! that was helpful! SA