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!

Powered by Vanilla. Made with Bootstrap.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.
Register now for the upcoming GATK Best Practices workshop, Feb 20-22 in Leuven, Belgium. Open to all comers! More info and signup at

Does UnifiedGenotyper use the first rs it finds at a given position ?

lindenblindenb FranceMember Posts: 52 ✭✭

Hi the GATK team;

I use the UnifiedGenotyper the following way:

java -jar GenomeAnalysisTK-2.1-13-g1706365/GenomeAnalysisTK.jar \
        -R /human_g1k_v37.fasta \
        -T UnifiedGenotyper \
        -glm BOTH \
        -S SILENT \
         -L ../align/capture.bed  \
         -I  myl.bam  \
        --dbsnp \
        -o output.vcf 

When I look at the generated VCF , the variation 18:55997929 (CTTCT/C) is said to be rs4149608

18 55997929 rs4149608 CTTCT C (...)

but in the dbsnp_135.b37.vcf.gz, you can see that the right rs## should be rs144384654

$ gunzip -c |grep -E -w '(rs4149608|rs144384654)'
18 55997929 rs4149608 CT C,CTTCT (...)
18 55997929 rs144384654 CTTCT C (...)

does UnifiedGenotyper uses the first rs## it finds at a given position ? Or should I use another method/tool to get the 'right' rs## ?

Thank you,


Best Answer


Sign In or Register to comment.