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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Variant Calling of a personal genome : USAGE question
I have been successfully dealing with GATK tools for variant calling for exome sequences, but now I have to do it for a personal genome. Since the genome has been sequenced in two runs , using 7 lanes per each run , now I have 28 fastq files.( paired end reads (2)* 7 lanes * 2 runs). I haven't deal with such a large number of files at once before. My suggested approach is to,
1) Align, Dedup, Realign and Recalibrate per lane. (So I get 14 aligned,deduped,realigned and reacalibrated bam files)
2) Merge the bam files inorder to produce a single bam file
3) Call variants using the single bam file using Haplotype Caller.
Do you think my approach is feasible? Or do you have any alternative approaches? Furthermore, what is the best tool to merge the bam files?
Thanks in advance.