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HaplotypeCaller gave different results if include --dbsnp argument

jacobhsujacobhsu Hong KongPosts: 6Member
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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