Avatar

Indrani Datta

Follow
  • Total activity 54
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 9

Posts

Recent activity by Indrani Datta Sort by recent activity Recent activity Votes

  • ModelSegments output from Somatic CNV

    1. Community
    2. General Discussion

    Dear GATK forum, I have performed somatic CNV analysis jointly with coverage data with ModelSegments with GATK 4.4.0.0 with hg38 with regular parameters and output from this run leads to figure 1 w...

    • Indrani Datta
    • 4 followers
    • 32 comments
    • 0 votes

  • FuncotateSegments

    1. Community
    2. General Discussion

    Dear GATK support, I tried to run  FuncotateSegments with gatk-4.4.0.0 and with funcotator_dataSources.v1.7.20200521s ( I am interested in hg38) but it is error out saying that  "A USER ERROR has o...

    • Indrani Datta
    • 2 followers
    • 2 comments
    • 0 votes

  • Somatic CNV workflow

    1. Community
    2. General Discussion

    Dear GATK forum, I have performed somatic CNV analysis jointly with allelic counts and coverage data with ModelSegments. The output is a segment file with many columns. My questions are: 1. Some of...

    • Indrani Datta
    • 2 followers
    • 1 comment
    • 0 votes

  • GATK ModelSegments result

    1. Community
    2. Somatic

    Dear GATK forum, I have performed somatic CNV analysis jointly with allelic counts and coverage data with ModelSegments. The output is a segment file with many columns. My questions are: 1. Some of...

    • Indrani Datta
    • 2 followers
    • 3 comments
    • 0 votes

  • PlotDenoisedCopyRatios Error

    1. Community
    2. Somatic

    REQUIRED for all errors and issues: GATK 4.3.0.0  gatk PlotDenoisedCopyRatios \    --standardized-copy-ratios /home/jupyter/notebooks/3-somatic-cna/sandbox/tumor.standardizedCR.tsv \    --denoised-...

    • Indrani Datta
    • 2 followers
    • 2 comments
    • 0 votes

  • GATK SelectVariants

    1. Community
    2. General Discussion

    Dear Community, Can GATK SelectVariants able to read a "bgz". Such as if I want to read a  gnomad file for subsetting , please let me know if GATK SelectVariants able to read a gnomad bgz file such...

    • Indrani Datta
    • 2 followers
    • 4 comments
    • 0 votes

  • Mutect2 -liquid biopsy

    1. Community
    2. General Discussion

    Hello GATK forum, I wanted to know if the usual best practices steps to call with Mutect2 on exome from human samples need any changes in analytical/best practices steps in case the sample is from ...

    • Indrani Datta
    • 2 followers
    • 5 comments
    • 0 votes

  • GATK Workshop

    1. Community
    2. General Discussion

    Hello, Please let me know if there will be any GATK workshop with Terra cloud platform- training in 2023. Thanks, Indrani

    • Indrani Datta
    • 5 followers
    • 17 comments
    • 0 votes

  • Somatic copy number variants (CNVs) and Panel of Normals creation

    1. Community
    2. Somatic

    Hello GATK help,   I am currently trying to understand the  workflow for Somatic copy number variants (CNVs). And I am interested to know if I only have one sample to analyze i,e 1 pair of normal &...

    • Indrani Datta
    • 3 followers
    • 6 comments
    • 0 votes