Tanya Sarkin Jain
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Activity overview
Latest activity by Tanya Sarkin Jain-
Tanya Sarkin Jain commented,
Sure - Command executed: gatk --java-options "-Xmx9830M -XX:-UsePerfData" \ HaplotypeCaller \ --input m21009_241011_231041.sorted.bam \ --output m21009_241011_231041.vcf.gz \...
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Tanya Sarkin Jain commented,
Was this issue resolved? I am getting the same issue but I should be using the latest release of GATK 4.5.0.0 and am seeing the process gets terminated always at the same point (chr19), with an exi...
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Tanya Sarkin Jain commented,
Thank you for the reply I'll have to check the depth, in my above post I was attempting to do the FilterMutectCalls with the pasted commands, however, the number of resulting records in the outputt...
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Tanya Sarkin Jain commented,
Thank you, further when I run filter mutect2 I see no changes. I am also running mutect with bqsr corrected, and though it is still running, based off the current numbers I don't expect the order o...
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Tanya Sarkin Jain created a post,
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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Tanya Sarkin Jain commented,
Thank you, from the documentation, that says: "The known variants are used to mask out bases at sites of real (expected) variation, to avoid counting real variants as errors. Outside of the masked ...
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Tanya Sarkin Jain created a post,
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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Tanya Sarkin Jain commented,
Im running the recalibration script again, and seemed to be getting further along (not crashing at NC_000008.11:117060763), though still curious what the issue could've been
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Tanya Sarkin Jain commented,
[Mon May 13 13:04:56 PDT 2024] Executing as tanyajain@qb3-id286.wynton.ucsf.edu on Linux 4.18.0-513.24.1.el8_9.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.10+7-LTS; Deflater: Intel; Inflater: Intel...
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Tanya Sarkin Jain created a post,
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...