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Muhammad Shoaib Akhtar

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Recent activity by Muhammad Shoaib Akhtar Sort by recent activity Recent activity Votes

  • GATK Germline CNV Discovery

    1. Community
    2. General Discussion

    This is just an exploratory question for my understanding. How GATK's germline CNV calling works in single sample mode vs cohort mode?

    • Muhammad Shoaib Akhtar
    • 2 followers
    • 1 comment
    • 0 votes

  • GATK tutorial workflows

    Answered
    1. Community
    2. General Discussion

    I have a basic question to GATK team: In GATK's best practices workflow guides, some workflows are shown. Are they copyright free? Can I reuse them to illustrate pipelines I used in my research? Fo...

    • Muhammad Shoaib Akhtar
    • 2 followers
    • 3 comments
    • 0 votes

  • Haplotypes of duplicated genes

    1. Community
    2. General Discussion

    I run GATK Pipeline for Germline Copy Number Variation 4.1.9.0 for targeted human sequences. I found many genes with CNVs as 3N, 4N or 5N. I want to haplotype those genes to identify sequences. Is ...

    • Muhammad Shoaib Akhtar
    • 3 followers
    • 6 comments
    • 0 votes

  • De novo assembly

    1. Community
    2. Germline

    Does GATK have any tool for de novo assembly?

    • Muhammad Shoaib Akhtar
    • 2 followers
    • 4 comments
    • 0 votes

  • Multi-sample VCF for CNV calling

    Answered
    1. Community
    2. General Discussion

    Hi, I'm using GATK 4.1.9.0 for Germline and Rare copy number variant discovery. I have a big dataset of more than 400 samples and I'm studying about 800 genes in each sample. I ran CNV pipeline suc...

    • Muhammad Shoaib Akhtar
    • 4 followers
    • 8 comments
    • 0 votes

  • Genome STRiP SV Preprocess

    1. Community
    2. Germline

    I tried to run SV Preprocess script as following and facing following error: Error: Could not find or load main class org.broadinstitute.gatk.queue.QCommandLineCaused by: java.lang.ClassNotFoundExc...

    • Muhammad Shoaib Akhtar
    • 2 followers
    • 11 comments
    • 0 votes

  • What is contig ploidy priors table and how to make it?

    Answered
    1. Community
    2. General Discussion

    I am using GATK 4.1.2.0.   For germline copy number variation analysis, I have to run GATK tool DetermineGermlineContigPloidy. I have high coverage target sequencing data. How I can make Contig Plo...

    • Muhammad Shoaib Akhtar
    • 8 followers
    • 17 comments
    • 0 votes

  • Difference between GATK Germline CNV Pipeline vs Genome STRiP?

    Answered
    1. Community
    2. Documentation Questions

    My dataset contains 400 individuals and I have to find CNVs. Which pipeline I should use GATK or Genome STRiP? More important is that how both these programs are different from each other? I am new...

    • Muhammad Shoaib Akhtar
    • 3 followers
    • 8 comments
    • 0 votes