Whole Genome GATK with uBAM files

Question

[abhishek.maj08]

Hi,

I am trying to run GATK on a whole genome. However my files (8) are in unmapped bam format. So do I have to merge the bam files first (Picard MergeSamFiles) into a single file before using BWA mem and subsequently MergeBamAlignment?

Also according to this tutorial (https://software.broadinstitute.org/gatk/documentation/article?id=6483) even though I have a uBam, I still have to convert it to fastq at an intermediate step. Is this because of Bwa Mem's input constraints?

Thanks

[WouterDeCoster]

Are those 8 files one sample or 8 samples?

Note that you can pipe the SamToFastq step directly to bwa mem: http://gatkforums.broadinstitute.org/gatk/discussion/6483/how-to-map-and-clean-up-short-read-sequence-data-efficiently#step3D

[abhishek.maj08]

All the eight files belong to the same animal, so one sample, different flow cells.

Answer 1

[d-cameron]

Also according to this tutorial (https://software.broadinstitute.org/gatk/documentation/article?id=6483) even though I have a uBam, I still have to convert it to fastq at an intermediate step. Is this because of Bwa Mem's input constraints?

Bwa supports uBAM as in input file format so FASTQ generation is not required, and is in fact, not done by the Broad Institute for their samples[1]. That said, their documentation does assume a FASTQ based pipeline:

In case you're wondering, we still show the FASTQ-based workflow as the default in most of our documentation because it is by far the most commonly-used workflow, and we want to keep the documentation accessible for our more novice users.

[1] http://gatkforums.broadinstitute.org/gatk/discussion/5990/what-is-ubam-and-why-is-it-better-than-fastq-for-storing-unmapped-sequence-data

[Brian Bushnell]

Oh, Broad. I wish they would give up on their ill-fated uBam format and start to care about efficiency.