So I am so curious which command and option should I use for RNA somatic calling.
Plus, if I have to use sommaticConfigure, I don't have normal sample (only tumor sample) for now,
so Can I use one of the random tumor cell for normal BAM in order exclude germline mutation?
If I tried to use the --rna in Somatic configuration, they told me I cannot use the --rna.
Also, RESA company required the prerequisite as a format for somatic calling like below:
conda activate strelka; python strelka-2.9.10.centos6_x86_64/bin/configureStrelkaGermlineWorkflow.py --bam alignment_minimap2/EGS-21-D2-NUC.bam --referenceFasta GRCh38.p12.genome.fa --rna --runDir ./strelka_out/EGS-21-D2-NUC_strelka_out; ./strelka_out/EGS-21-D2-NUC_strelka_out/runWorkflow.py -m local -j 4
So I am so curious which command and option should I use for RNA somatic calling.
Plus, if I have to use sommaticConfigure, I don't have normal sample (only tumor sample) for now, so Can I use one of the random tumor cell for normal BAM in order exclude germline mutation?
Thank you.