The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

#### ☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# Data Processing Pipeline: re-aligning from BAMs

Member Posts: 9
edited January 2013

I had a question that, while it might be more appropriate for a BWA or seqanswers audience, I noticed something in the GATK's "Data Processing Pipeline" under "Methods and Workflows" that made me wonder. The pipeline is described here and there's a nice flowchart as well:

The process describes a BAM of reads that are either not aligned or aligned by some process you don't want to use, so the first step seems to be Picard's RevertSam and then a realignment with BWA. I'm wondering why the process described by this GATK document splits it into per-lane BAM files. There doesn't seem to be any process done at the per-lane level other than BWA alignment. I have two guesses.. the first was to allow more parallelization at that step.

But my second guess is that perhaps BWA doesn't play nice with read groups when reading reads from BAM input files. If that is true, that would explain why I'm having trouble with BAM (a single sample, multiple lanes, merged into one file) -> BWA -> realigned-BAM -> GATK (either UnifiedGenotyper or RealignerTargetCreator, etc)--somewhere along the way, read groups are getting lost. So my guess is that the above-described pipeline splits it per-lane so it can manually respecify read groups all over again to BWA?

Is that other people's experience as well?

Also, the Methods and Workflows page describes a Queue script, but there's no link or anything to the actual Queue script. Anyone know where to find it?

Danny

Post edited by Geraldine_VdAuwera on

Danny Park, PhD -- Broad Institute, IDI, Sabeti Lab

Tagged:

• Charlestown, MAMember Posts: 274 admin

Hey Danny,

you are right on both reasons, but in the reverse order of importance.

1. BWA wipes out all RG information so if you try to realign a whole bam that has several @RG entries (1 per lane at least) it will be impossible (or at the very least a nightmare) to reassign read groups to the appropriate reads. Doing it per lane, I can simply assign every read in each aligned bam to a single Read Group and later join them all.

2. Smaller BAMs usually mean we can run on a faster queue and get jobs done faster. But this is really not the main reason to do this. It is reason #1. Joining everything afterwards makes any gains we get here from splitting irrelevant.

Geraldine Van der Auwera, PhD

• Charlestown, MAMember Posts: 274 admin