We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

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

Hello.

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.

Answers

Sign In or Register to comment.