We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

Determine somatic mutations, INDEL, CNV in cfDNA of Pancreatic Cysts Fluid (20 Fastq files)

BegaliBegali GermanyMember ✭✭


For 20 samples of cfDNA for 20 patietns, I would like to discover somatic mutations, INDEL, CNV for cancer as what I understood :smile: :
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 \
-O sandbox/combined-normals.tsv
java -jar GATK$.jar CreatePanelOfNormals \
-I sandbox/combined-normals.tsv \
-O sandbox/normals.pon \
-noQC \
--disableSpark \
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

Best Answers


Sign In or Register to comment.