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.

dbsnp file in unified genotyper

Hi,

I am using unified genotyper utility of GATK.
I don't exactly know how I should make the dbsnp file necessary. I thank you very much for any help.

Regards,
Homa

Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    I'm sorry, I don't understand your question. The dbsnp file is not required by the UnifiedGenotyper but it can be used if you want. Are you trying to use it and it's not working? Or is your problem something else?

  • namsyvonamsyvo University of MemphisMember
    edited April 2014

    I want to make sure about one problem related to this topic. As I understand from the GATK-UGT document, dbSNP files are not used to verify called SNPs in any way while performing SNP calling with GATK-UGT, is that correct?

    --dbsnp / -D
    dbSNP file
    rsIDs from this file are used to populate the ID column of the output. Also, the DB INFO flag will be set when appropriate. dbSNP is not used in any way for the calculations themselves.
    --dbsnp binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3

    Nam.

    Post edited by namsyvo on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Nam, they are used only for annotating the rsID if a variant has been reported previously. They are not used in any way to decide whether variants should be emitted.

  • namsyvonamsyvo University of MemphisMember

    Thank you for your previous answer. I have one more question, if I provide GATK a VCF file with the option --alleles (together with setting genotyping_mode to be GENOTYPE_GIVEN_ALLELES), is this information used for the calculation of SNP calls, or the determination of qualities of SNP calls, or whatever related to the process of calling SNPs?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @namsyvo‌

    Hi,

    Normally our variant caller tools find candidate alleles in the data. When you provide a -alleles file, the variant caller will use the alleles specified for that position in the file (including the reference allele). If a sample does not have any of the alternate alleles specified at the position, it will simply be genotyped as homozygous reference. The quality scores of a variant site are calculated in the same way as not specifying a -alleles file.

    The usual rules for whether to emit a call or not (if no sample is variant at the site, don't emit a call unless -allSites is specified) still apply.

    I hope this helps.

    -Sheila

Sign In or Register to comment.