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Which command to use for somatic calling and RNA sequencing? #223

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HyojeenLee opened this issue Dec 2, 2022 · 0 comments
Open

Which command to use for somatic calling and RNA sequencing? #223

HyojeenLee opened this issue Dec 2, 2022 · 0 comments

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@HyojeenLee
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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.

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