day to day activity for mutation data The scripts are usually the day to day activity that is performed for any exome project for normal/tumor paired samples. This is usually done after the mutations are called, for normal/tumor pair I prefer using VarScan2 and Mutect.
Am using CNV tools on these data like ADTex , Control-FREEC, VarScan2 CBS, ExomeCNV
For running the rna seq variant pipeline one can simply follow
./rna_seq_variant_pipeline.sh <output_basename> <fastq folder> <output_folder_loc> [cpus]
Example:
./rna_seq_variant_pipeline.sh test_sample /illumina/fastq/sample_folder /path_to/rnaseq/variants/out 12