HaplotypeCaller gave different results if include --dbsnp argument

jacobhsujacobhsu Hong KongPosts: 9Member
edited November 2013 in Ask the GATK team

Hi, I used following commands to call variants from exactly the same file by HaplotypeCaller. However, I got different results. The results from case1 are not consistent to case2. In some chromosomes, the numbers of variants in case 1 are more than case 2, but others are less. The differences are only a few variants in each chromosome. Any idea? I supposed they will be the same because just adding --dbsnp information.


${java7} -jar $GATK/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -R $reference_genome \ -I $input_file \ -L X \ --genotyping_mode DISCOVERY \ -stand_emit_conf 10 \ -stand_call_conf 50 \ -o vcf_out/chrX.vcf


${java7} -jar $GATK/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -R $reference_genome \ -I $input_file \ -L X \ -nct 8 \ --dbsnp $dbsnp \ --genotyping_mode DISCOVERY \ -stand_emit_conf 10 \ -stand_call_conf 50 \ -o vcf_out/chrX.vcf

Post edited by jacobhsu on

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