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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 broadinstitute.org/bundle/1.5/b37/dbsnp_135.b37.vcf.gz \ -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 broadinstitute.org/bundle/1.5/b37/dbsnp_135.b37.vcf.gz |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## ?