Dear Sir,
am new and currently trying to learn 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 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 is downloaded from here
https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files
GRCh38.d1.vd1.fa.tar.gz
was able to complete the Genome Alignment and Alignment Co-Cleaning, next wanted to do the variant calling step, in the next using MuSe
MuSE call -f -r <tumor.bam> <normal.bam> -O <intermediate_muse_call.txt>
I don't know what the region is (is it the chromosome number, or the read group)
also how to prepare the normal.bam and tumor.bam files. Please help.
Thanks
Dr. Prabhakar
