I am trying to detect RNA editing differences between RNASeq normal and tumor samples from the same individual, but I am a bit confused about the list(s) of SNV to use.
I am using the following strategy but not sure if it is correct:
(1) detect germline mutations from normal (with GATK HaplotypeCaller)
(2) detect germline and somatic mutations from tumor (with GATK Mutect2)
(3) Discard homozygous variants
(4) Annotate the variants and tag the ones present in dbSNP and COSMIC databases
(5) Call RNA editing sites in normal and tumor separately with their respective lists
(6) Check which sites are present in tumor but not in normal.
Questions:
Variants present in dbSNP and COSMIC (tagged as "1") will be filtered out by GIREMI, right?
For the tumor sample, should I use instead the germline SNV list obtained from the normal sample (since it is the same individual) and just add the somatic variants detected?
Or, for the tumor sample, call the germline variants in the tumor sample with the same program as the normal sample and then call the somatic variants with Mutect and add them together to the tumor SNV list?
Should I include germline and somatic variants called from the DNA of these sample as well?
Hi,
I am trying to detect RNA editing differences between RNASeq normal and tumor samples from the same individual, but I am a bit confused about the list(s) of SNV to use.
I am using the following strategy but not sure if it is correct: (1) detect germline mutations from normal (with GATK HaplotypeCaller) (2) detect germline and somatic mutations from tumor (with GATK Mutect2) (3) Discard homozygous variants (4) Annotate the variants and tag the ones present in dbSNP and COSMIC databases (5) Call RNA editing sites in normal and tumor separately with their respective lists (6) Check which sites are present in tumor but not in normal.
Questions:
Thanks !