Tanya Sarkin Jain
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Recent activity by Tanya Sarkin Jain Sort by recent activity-
Mutect2 resulting variant numbers
Hello, I am using gatk/4.5.0.0. I am getting a really large number of variants between my crispr edited and non-edited sample (same cell line), which seems off. I wanted to check in about this be...
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BQSR Score recalibration for NovaSeq Data
Hi, I am working with reads generated from NovaSeq 6000 System, where read quality scores are generated by w Real Time Analysis 3 (RTA3) software. In this pipeline, quality scores are binned into 3...
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BQSR error
REQUIRED for all errors and issues: a) GATK version used: gatk/4.5.0.0 b) Exact command used: I am running this shell script: #! /usr/bin/env bash # # lines starting with #$ i...
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Using Mutect 2 - question about Germline var, and PON
Hi, I am aiming to use Mutect2, I see that it requires a germline-resource. I see one on the google bucket that is from 2017 - is there a newer one? Further my mapped bam, have NCBI annotations, cu...
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(new user) Question about BAM preparation and MUTECT 2 for special use
gatk/4.2.3.0 I want to use Mutect2 to compare a cell line that has been edited, with its control before editing. Was thinking that Mutect2 could be used for this purpose. I understand that accordin...