Muhammad Shoaib Akhtar

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Recent activity by Muhammad Shoaib Akhtar Sort by recent activity Recent activity Votes
  • GATK Germline CNV Discovery

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

  • GATK tutorial workflows


    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...

  • Haplotypes of duplicated genes

    I run GATK Pipeline for Germline Copy Number Variation 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 ...

  • De novo assembly

    Does GATK have any tool for de novo assembly?

  • Multi-sample VCF for CNV calling


    Hi, I'm using GATK 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...

  • Genome STRiP SV Preprocess

    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...

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


    I am using GATK   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...

  • Difference between GATK Germline CNV Pipeline vs Genome STRiP?


    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...