The current GATK version is 3.8-0
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.

Got a problem?


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
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

VariantFiltration for non-human data

sagipolanisagipolani Member
edited October 2012 in Ask the GATK team

Hi all,

I'm currently analysing non-human mammalian whole genome data (>30x). No previous variants databases are available.

I'm currently in the VariantFiltration step. I came around the following command which is used for human data, and I'm wondering if it will be good for non-human data:

java -Xmx10g -jar GenomeAnalysisTK.jar \
-R [reference.fasta] \
-T VariantFiltration \
--variant [input.recalibrated.vcf] \
-o [recalibrated.filtered.vcf] \
--clusterWindowSize 10 \
--filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" \
--filterName "HARD_TO_VALIDATE" \
--filterExpression "DP < 5 " \
--filterName "LowCoverage" \
--filterExpression "QUAL < 30.0 " \
--filterName "VeryLowQual" \
--filterExpression "QUAL > 30.0 && QUAL < 50.0 " \
--filterName "LowQual" \
--filterExpression "QD < 1.5 " \
--filterName "LowQD" \
--filterExpression "SB > -10.0 " \
--filterName "StrandBias"

I would appreciate your thoughts on this matter.

Thank you very much!

Sagi

Post edited by Geraldine_VdAuwera on

Best Answer

Answers

  • xujingxujing ChinaMember

    Hi all,
    I had saw a command about GATK/VariantFiltration/filterExpression. I cannot understand the meaning of some arguments in the below command. The command is --filterExpression "QD < 20.0 || ReadPosRankSum < -8.0 || FS > 10.0 || QUAL < $MEANQUAL" I want to know the meaning of the bold fonts. Can you help me?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @xujing,

    Please read the documentation on JEXL expressions. Use the search box in the top right corner of the page if you don't know where to find the documentation.

Sign In or Register to comment.