We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
How can i do alignment to my fastq data?
I got several fastq data, and i just read some pipeline you guys released here.
And i don't which way is better to do alignment.
One way should be like this:
i should convert the fastq data into ubam, then i just use the picard's SamToFastq and bwa to do the alignment jobs. After that, i think i should use MergeBamAlignment to merge my sam file. Then i can use picard's MergeSamFiles or samtools to merge all my sam files.
The other way should be like this:
i just use the bwa to align my fastq file into bam file, and i just use picard's MergeSamFiles or samtools to merge them.
which is better? Dose these two ways get huge difference?
Thanks a lot !!!