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.

mRNAseq and SNPs call, how can we make this as good as possible?

myoglumyoglu Member
edited October 2013 in Ask the GATK team

Hi!
I have worked some time on a mRNAseq set, single-end. Its a high quality set and lots of biological replicates (200+).

My question is, how could I best contribute to the methodology used for SNPs call in mRNAseq? What do we need tested to improve this method?

Answers

  • Hi,
    I'm working on testing and creating a best practices pipeline for RNAseq data and I would be happy to hear and learn what tools and protocol do you use. What do you consider to be hight quality set and how do you evaluate your results. We can discuss it here in the forum or in email, whatever you prefer.

    Thanks,
    Ami

  • Hi!
    I have just started the testing and this is my first meeting with NGS, so much is new to me.

    So far I have:
    Tophat 2 -> different pre. pros. w/ Picard -> GATK "best practise" or Samtools -> Total called SNPs evaluation against each other, dpSNP and 1000G .

    Im planning on doing the same with BWA. Also I want to tweak the settings of Haplotype caller more. My computer setup is kinda slow, so doing a lot of test takes time. Thats why I was asking here, so I don't waste time doing something obvious.

    I consider my set high quality after FastQC evaluation: 50mill. depth, 51bp length, systematic GC content typical of Illumina 2500, no quality drop from 1-51bp, no Kmer problems. Duplication levels are typical of mRNAseq, but how to handle that is still an issue.

    Thanks!

Sign In or Register to comment.