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how to use matched-normal in germline calling with GATK3 ver.


I have 30 matched-normal bladder tumor(bam).

According to definition of germline variant, I use normal bam only to call germline variant using haplotypecaller. But there is no step to filter somatic variant. I guess it's necessary step to filter somatic variants among germline variants.

Steps I did--------------------------------------
1) Haplotypecaller; variant calling with gvcf mode
2) GenotypeGVCFs; Joint vcfs
3) VariantRecalibrator and ApplyRecalibration; Filtering variants.

Thanks in advance.


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