Muhammad Shoaib Akhtar
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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 workflowsAnswered
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 188.8.131.52 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 callingAnswered
Hi, I'm using GATK 184.108.40.206 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?Answered
I am using GATK 220.127.116.11. 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?Answered
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...