What are the initial files required in order to go through the Data Preprocessing, Variant Discovery and IGV phases of Genomic analysis?
Answered
Hello,
I am using GATK4 and I have downloaded and installed all the prior tools needed for the pipeline (Picard, BWA, SAM). Please pardon my question if it is not proper. According to the tutorials and Best Practice workflow, we need a FASTQ file or uBAM file to start with Preprocessing. But, when I use the tool BWA, it says it needs both FASTA and FASTQ file to generate SAM file (tool: bwa mem or bwa aln). I am confused as to which files to download in order to practice using GATK. Also, if possible, please provide a link to any open dataset using which I could try practicing the tool.
Thank you so much.
Regards,
Kountay Dwivedi
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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? I am unable to find dataset using which I could at least try phase 1 and 2.Thank you.
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Here is more information about our resource bundle publicly available:
And our tutorials:
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