sanjeevksh
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Activity overview
Latest activity by sanjeevksh-
sanjeevksh commented,
Hi Anthony (Anthony Dias-Ciarla) Thank you for your feedback. I have used CombineGVCFs several times before for combining GVCFs from multiple samples but didn't realise it can be used for concatena...
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sanjeevksh created a post,
GatherVcfs to concatenate GVCFs
GATK version used: gatk4-4.2.6.1-0/gatk-package-4.2.6.1 Dear GATK experts,I am trying to concatenate multiple GVCFs (all same samples, different genomic intervals) but having the following error: A...
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sanjeevksh commented,
Thanks Genevieve, that's very helpful! Kind regards, Sanjeev
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sanjeevksh created a post,
"NotDuplicateReadFilter" behaviour in HaplotypeCaller
AnsweredDear Team GATK, The description for "NotDuplicateReadFilter" read filter says it filters out reads marked as duplicate. Is it the right inference that this read filter will ONLY remove duplicate re...
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sanjeevksh commented,
Hi Genevieve, That's excellent! thank you for chasing this up and the update. Kind regards, Sanjeev
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sanjeevksh commented,
Hi Genevieve, Thank you for your feedback, this is very helpful! Kind regards, Sanjeev
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sanjeevksh commented,
Hi Genevieve, I also get such warnings for QD filter but only for few iterations (log provided below). I trust this is okay but still your confirmation will help. Kind regards, Sanjeev 12:45:31....
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sanjeevksh commented,
Thanks again for confirming this, I will stick to CombineGVCFs then :-) Kind regards, Sanjeev
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sanjeevksh commented,
Hi Genevieve, This is good that I checked this with you because I see no mention of GenomicsDBImport compatibility with diploids only in the tool description. Hopefully, the next steps would also w...
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sanjeevksh commented,
Hi Genevieve, Thank you so much for investigating this issue at your end and suggesting the possible solutions. I have tried option 2 and it worked absolutely fine. As a backup plan I also started ...