Avatar

Tanya Sarkin Jain

Follow
  • Total activity 18
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 7

Activity overview

Latest activity by Tanya Sarkin Jain
  • Avatar

    Tanya Sarkin Jain commented,

    1. Community
    2. General Discussion
    3. Mutect2 resulting variant numbers

    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...

  • Avatar

    Tanya Sarkin Jain commented,

    1. Community
    2. General Discussion
    3. Mutect2 resulting variant numbers

    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...

  • Avatar

    Tanya Sarkin Jain created a post,

    Mutect2 resulting variant numbers

    1. Community
    2. General Discussion

    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...

    • Tanya Sarkin Jain
    • Edited
    • 2 followers
    • 5 comments
    • 0 votes
  • Avatar

    Tanya Sarkin Jain commented,

    1. Community
    2. General Discussion
    3. (new user) Question about BAM preparation and MUTECT 2 for special use

    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 ...

  • Avatar

    Tanya Sarkin Jain created a post,

    BQSR Score recalibration for NovaSeq Data

    1. Community
    2. General Discussion

    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...

    • Tanya Sarkin Jain
    • Edited
    • 2 followers
    • 1 comment
    • 0 votes
  • Avatar

    Tanya Sarkin Jain commented,

    1. Community
    2. New User Advice
    3. BQSR error

    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

  • Avatar

    Tanya Sarkin Jain commented,

    1. Community
    2. New User Advice
    3. BQSR error

    [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...

  • Avatar

    Tanya Sarkin Jain created a post,

    BQSR error

    1. Community
    2. New User Advice

    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...

    • Tanya Sarkin Jain
    • Edited
    • 2 followers
    • 4 comments
    • 0 votes
  • Avatar

    Tanya Sarkin Jain created a post,

    Using Mutect 2 - question about Germline var, and PON

    1. Community
    2. General Discussion

    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...

    • Tanya Sarkin Jain
    • Edited
    • 4 followers
    • 1 comment
    • 0 votes
  • Avatar

    Tanya Sarkin Jain commented,

    1. Community
    2. General Discussion
    3. (new user) Question about BAM preparation and MUTECT 2 for special use

    Thank you - do you have any recommendations to what to look for when doing the comparison? Best, Tanya