We are currently working on whole exome analysis of breast cancer samples using the GDC Bioinformatics Pipeline https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
The tumor data .bam file was downloaded from GDC legacy archives. https://portal.gdc.cancer.gov/legacy-archive/files/9efa8d39-37e0-4236-9737-e14ddcfd93ff
The reference genome was downloaded from here https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files GRCh38.d1.vd1.fa.tar.gz
We were able to complete the Genome Alignment and Alignment Co-Cleaning, next wanted to do the variant calling and copy number variation.
In order to perform variant calling and copy number variation do we need normal exome data (or not), is there any publicly available normal exome data for using it for variant calling and copy number variation.
And is it OK to use any other normal exome data that was not obtained from the same study.
Or is it mandatory to use the normal exome data from the same study (what if the normal exome data is not available from the same study).
Thanks Dr. Prabhakar