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Whole genome sequence analysis pipeline

Hello, everyone.

I am new to bioinformatics. Currently, I want to analyze whole genome sequence data from GTEx bam files. But I have no idea about how to start? I googled a lot, but cannot find a tutorial for a beginner? Could you please provide any suggestions for me? Thank you in advance.

snp next-gen sequencing
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written by panxingxin16 • panxingxin16

GTEx profiled transcriptomes, not genomes. Are you aware of this fact?

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written by Kevin Blighe Kevin Blighe

Are you sure? According to Gtex p8 release, there are hundreds of WGS data.....Please correct me if I misunderstood it.

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written by panxingxin16 • panxingxin16

No no, please correct me if I mis-understood. Can you provide a link?

If you are a beginner in this space, you should start with the GATK, but make sure that you now use > version 4 of the GATK.

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written by Kevin Blighe Kevin Blighe

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