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Determine somatic mutations, INDEL, CNV in cfDNA of Pancreatic Cysts Fluid (20 Fastq files)
For 20 samples of cfDNA for 20 patietns, I would like to discover somatic mutations, INDEL, CNV for cancer as what I understood :
1- Preprocessing data mapping by bwa mem using hg38 as reference genome in order to generate BAM files then combine them.
2- Processing data based on -T MuTect2 ( Calling somatic mutations, INDEL) but you mean by those two parameters
-I:normal normal.bam, which I read that file belong to the same sample which I did not have it or how can I generate it should be different ones that will be obtained by bwa mem .The second parameter is --cosmic COSMIC.vcf.
3-For CNVs what meaning of -T
actually all those parameters explanation
java -jar GATK4.jar CombineReadCounts \
-inputList normals.txt \
java -jar GATK$.jar CreatePanelOfNormals \
-I sandbox/combined-normals.tsv \
-O sandbox/normals.pon \
what I got each -I means insert or input but I do not know what they are...
can you please give me some hints!!!
Another Q why calling somatic mutations, INDEl is difference of CNVs :::
Thanks in advance