Saba
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Activity overview
Latest activity by Saba-
Saba commented,
Genevieve Brandt (she/her) Many thanks for explaining that to me. It does make a lot of sense. Do you recommend using this AF value as VAF to make the clinical decisions ( in patients report) or ca...
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Saba commented,
David Benjamin In contrast to the above examples, I have a few examples which are picked up by mutect2 at a very very low alt count, i.e 2/8, 3/311, and 4/97. Please see these: HOXA13 - 4/97 ...
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Saba commented,
David Benjamin Thank you so much for fixing this issue. Much appreciated. I have used the google bucket jar to test my 4 samples where we knew this issue existed. Here are my results and then a q...
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Saba created a post,
Mutect2 - VCF
Answereda) GATK version used: 4.1.7b) Exact command used: getShell("{gatk} FilterMutectCalls -V {input.unfiltered} -R {params.hg} --contamination-table {input.ctTable} --tumor-segmentation {input.segTable}...
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Saba commented,
Hi @David, Please find the link with the bam files for a sample having missing KRAS (KRAS with 3% alternate bases: 40/1182 Alternate allele). https://www.dropbox.com/sh/utp3wtpaf6amfys/AABv5TPRsN...
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Saba commented,
David Benjamin, David Benjamin Yeah, it would be really helpful getting response on this matter, please. I am still waiting for that.
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Saba commented,
David Benjamin Many thanks for your suggestions. I have tried 2 things: Ran the samples with the option -dont-use-soft-clipped-bases true \ Switching this option on didn't help to pick u...
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Saba created a post,
Mutect2 MISSING Low Frequency key (TP53 and KRAS) mutations
Dear GATK Team, We have noticed that Mutect2 ( 4.1.4.0) is missing some of the key (TP53 and KRAS) mutations from tumor-normal paired cfDNA somatic mutation calling. We have an analysis from ano...