Avatar

Shivangi Agarwal

Follow
  • Total activity 19
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 5

Activity overview

Latest activity by Shivangi Agarwal
  • Avatar

    Shivangi Agarwal commented,

    1. Community
    2. Somatic
    3. Mutect2 -could not detect expected Indels

    Okay, thanks. I am looking into it and will get back to you soon.       Thanks, Shivangi

    • View comment
    • Shivangi Agarwal
    • 0 votes
  • Avatar

    Shivangi Agarwal created a post,

    Mutect2 -could not detect expected Indels

    1. Community
    2. Somatic

    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: Hi GATK team, I am calling somatic variants using Mutect2 for 10 samples. I could see lots o...

    • Shivangi Agarwal
    • 2 followers
    • 2 comments
    • 0 votes
  • Avatar

    Shivangi Agarwal commented,

    1. Community
    2. Somatic
    3. Huge number of variants in tumor only mode as compared to T/N paired mode using Mutect2

    Hi David,  Thanks so much for your response. I did call variants both ways (1st: no germline and no public PON and IInd: Germline: somatic-b37_af-only-gnomad.raw.sites.vcf & PON somatic-b37_Mutect2...

    • View comment
    • Shivangi Agarwal
    • 0 votes
  • Avatar

    Shivangi Agarwal created a post,

    Huge number of variants in tumor only mode as compared to T/N paired mode using Mutect2

    1. Community
    2. Somatic

    REQUIRED for all errors and issues: a) GATK version used:4.2.2.0b) Exact command used: c) Entire program log: Hi GATK team, I want to call somatic variants for 60 samples in tumor-normal paired mo...

    • Shivangi Agarwal
    • 3 followers
    • 3 comments
    • 0 votes
  • Avatar

    Shivangi Agarwal created a post,

    af-only-gnomad.vcf.gz

    1. Community
    2. Somatic

    REQUIRED for all errors and issues: a) GATK version used: b) Exact command used: c) Entire program log: Hi GATK experts, I want to download af-only-gnomad.vcf.gz to CreateSomaticPanelsofNormals. I...

    • Shivangi Agarwal
    • 2 followers
    • 1 comment
    • 0 votes
  • Avatar

    Shivangi Agarwal commented,

    1. Community
    2. Other
    3. Error in running GenomicsDBConfigException

    Hi Genevieve, I have a few questions regarding my GATK run set up. These are as: 1. I have 12 normal samples. Can I make my own PON taking those twelve ? I mean is it allowed or recommended ? Does ...

    • View comment
    • Shivangi Agarwal
    • 0 votes
  • Avatar

    Shivangi Agarwal commented,

    1. Community
    2. General Discussion
    3. Variant calling for matched samples

    Hey Genevieve Brandt, Can you please spare some time to answer my query as mentioned above ? I need to run this analysis at the earliest.     Thanks and regards Shivangi Agarwal

    • View comment
    • Shivangi Agarwal
    • 0 votes
  • Avatar

    Shivangi Agarwal created a post,

    Variant calling for matched samples

    Answered
    1. Community
    2. General Discussion

    Hi, I want to call variants for my 36 samples each of which is having normal data. The samples are matched normal. Please let me know how to correctly run GATK and what are the steps for this ? My ...

    • Shivangi Agarwal
    • 2 followers
    • 3 comments
    • 0 votes
  • Avatar

    Shivangi Agarwal commented,

    1. Community
    2. Other
    3. Error in running GenomicsDBConfigException

    Hi Genevieve,   Can you please respond to the above query.   Thanks

    • View comment
    • Shivangi Agarwal
    • 0 votes
  • Avatar

    Shivangi Agarwal commented,

    1. Community
    2. Other
    3. Error in running GenomicsDBConfigException

    Hi Genevieve, I want to call variants for my samples which are divided into four categories as normal, stage I, stage II and stage III. My understanding till now after going through multiple docume...

    • View comment
    • Shivangi Agarwal
    • 0 votes