1. Tool Index
2. 4.0.11.0
3. SamToFastq (Picard)

Kindly let us know of a tool that converts FASTQ to uBAM for that is needed in Data Preprocessing phase of GATK Best Practices.

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• Kountay Dwivedi
• November 11, 2020 05:38
• 0 votes

1. Community
2. Documentation Questions
3. How do I obtain fastq files from a bam file?

Hi Maguelonne , Would it be possible for you share the details of sample dataset that you're using, if any?I am unable to find proper sample data over which I could practice GATK Best Practices. Th...

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• Kountay Dwivedi
• November 11, 2020 04:45
• 0 votes

1. Community
2. Documentation Questions
3. How do I obtain fastq files from a bam file?

Hi, I am also having an issue regarding conversion of .fq to .sam/.bam In the GATK Best Practices, in order to execute the step MergeBamAlignment, we need a uBam file and aligned bam file. However,...

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• Kountay Dwivedi
• November 11, 2020 04:35
• 0 votes

1. Community
2. Documentation Questions
3. What are the initial files required in order to go through the Data Preprocessing, Variant Discovery and IGV phases of Genomic analysis?

Hi Genevieve Brandt ,Thank you so much for taking out your time. Could you please provide me a link to practice dataset, using which I could actually start practising the GATK Best Practices phases...

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• Kountay Dwivedi
• October 25, 2020 18:09
• 0 votes

1. Getting Started
2. Best Practices Workflows
3. Data pre-processing for variant discovery

Hi, I am a Junior Researcher, and I need to familiarise myself with GATK Best Practices. But I cannot find out sample dataset to test Data Pre-processing. Please help me out. Thanks. 

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• Kountay Dwivedi
• October 24, 2020 17:38
• 5 votes