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Highly different number of SNPs between Unifiedgenotyper and Haplotypecaller in mydata.

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I ran two different SNP callers to compare my data but they showed highly different numbers of SNPs.

for Unifiedgenotyper
java -Xmx48g -jar GenomeAnalysisTK.jar -T UnifiedGenotyper -drf DuplicateRead -R HOchinense.fasta -I ./PBHO/PB_sorted.bam -o ./PBHO/PB_raw.vcf -glm BOTH

for Haplotypecaller
java -Xmx48g -jar GenomeAnalysisTK.jar -T HaplotypeCaller -drf DuplicateRead -R HOchinense.fasta -I ./PBHO/PB_sorted.bam -o ./PBHO/PB_raw.vcf -bamout ./PBHO/bamout.bam

the number of SNPs using UG is 10 times higher than that using HC.

I think I made a mistake but I cannot figure out it.

Could you let me know what I make a mistake?

Thanks for reply.

HTKIM


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