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