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

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