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!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
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.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

How well does BWA/GATK work with sequences that are >20% divergent?

ktretinaktretina Baltimore, MDMember
edited July 2013 in Ask the GATK team

I have the genomes of several isolates of a parasite, and I would like to investigate synonymous/non-synonymous substitution for identifying potential antigens, as well as SNPs genome-wide and I am wondering how well BWA/GATK are suited for this purpose. I've been told that BWA is only very good with sequences <2% divergent, and some of the antigens in this specie are known to be >20% divergent. However, I also know that GATK does local realignments of indels. So I would specifically like to know - is BWA/GATK good for looking at substitutions/SNPs in highly variable genes, and if not which other alignment tools are compatible and appropriate for this purpose?

Best Answer

Answers

Sign In or Register to comment.