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 2.9.0 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.

what "mode" should I use for VariantRecalibrator?

rcholicrcholic DenverPosts: 68

For exome-sequencing, I was wondering how I should decide the "-mode" parameter? should I use "SNP" or "Indel" or both? I want to get both information in the final results, should I use "BOTH" -mode?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,743 admin

    Use of the BOTH mode is no longer recommended, so please don't use that.

    You should recalibrate the two types of variants separately. The recommended workflow (described in the VQSR tutorial here) is to first recalibrate for one type of variant (eg the snps, using -mode SNP), then recalibrate the resulting VCF file for the other type (eg the indels, using -mode INDEL). When you recalibrate for one type, the variants of the other type are emitted to the output file without modification. This way you don't have to separate them into different files before recalibration.

    Geraldine Van der Auwera, PhD

  • rcholicrcholic DenverPosts: 68

    Thanks Geraldine. Can i use the vcf file from haplotypecaller to do snp and indel recalibration separately? Or you recommend recalibration in a sequential one-after-another order?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,743 admin

    We recommend the sequential-order workflow because it is the most efficient, but you can modify the workflow to suit your needs, sure.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.