UnifiedGenotyper (UG) vs HaplotypeCaller (HC)

qq66zhangqq66zhang Posts: 1Member
edited May 2013 in Ask the GATK team

Hello GATK team,

I recently ran both caller on the same bam file. However, I got significantly less calls using HC (2844), vs UG (9676 snp mode, 860 indel mode). The version of GATK is GenomeAnalysisTK-nightly-2013-04-23-ga4d6edb, and the command used are:

# ##Variant calling using Haplotypecaller##
# $JAVADIR/java -Xmx2G -jar $GATK2DIR/GenomeAnalysisTK.jar \
#   -T HaplotypeCaller \
#   -R $HG19REF \
#   -I s_${1}.newRG.realigned.recal.bam \
#   --dbsnp $SNP137 \
#   -L $TARGETFILE \
#   -stand_emit_conf 10.0 \
#   -rf BadCigar \
#   -o s_${1}.HC.vcf
# 

# 
# ##Variant calling using UnifiedGenotyper##
# $JAVADIR/java -Xmx2G -jar $GATK2DIR/GenomeAnalysisTK.jar \
#   -T UnifiedGenotyper \
#   -R $HG19REF \
#   -I s_${1}.newRG.realigned.recal.bam \
#   --dbsnp $SNP137 \
#   -L $TARGETFILE \
#   -stand_emit_conf 10.0 \
#   -rf BadCigar \
#   -glm SNP \
#   -o s_${1}.UGSNP.vcf
# 
# 
#   
# ##Variant calling using UnifiedGenotyper##
# $JAVADIR/java -Xmx2G -jar $GATK2DIR/GenomeAnalysisTK.jar \
#   -T UnifiedGenotyper \
#   -R $HG19REF \
#   -I s_${1}.newRG.realigned.recal.bam \
#   --dbsnp $SNP137 \
#   -L $TARGETFILE \
#   -stand_emit_conf 10.0 \
#   -rf BadCigar \
#   -glm INDEL \
#   -o s_${1}.UGIndel.vcf
# 

Can anyone explain it to me what could went wrong.

Thanks!!

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,043Administrator, GATK Dev admin

    Hi there,

    Have you looked at some of the variants that are called by UG but not by HC? Can you tell if they look like real variants or not?

    Geraldine Van der Auwera, PhD

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