If you happen to see a question you know the answer to, please do chime in and help your fellow community members. 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.
sample prepared from multiple flowcell and multiple lanes
I have multiple paired-end fastqs from a single biological sample that was prepared by three flowcells, two lanes each.
In short, I have
where R1, R2 are paired-end reads.
I'm trying to generate a single bam file from these fastqs with bwa mem and samtools on reference GRCh37
Then ultimately run whole exome sequencing with following procedure.
bwa_mem for each 6 sets of paired-end reads
samtools sort for each 6 generated bams
samtools merge -r for the 6 generated bams to produce a single bam
Then start the GATK process on the merged.bam
and so on ...
I am not sure what is the best way to merge these fastqs and generate a single bam.
Could you recommend me how I should generate a single bam from these fastqs?