I have three somatic variants (mutations) detected in a single tumour sample. They come from Whole Genome Sequencing technologies and to call them normal and tumour samples were compared.
The mutations are supported by the same reads. It's a bit suspicious to me because this could indicate that the reads are from another part of the genome.
I have been searching a LOT for online tutorials about manual inspection of mutations with IGV. But I only found a couple of them that are interesting. However, I could not identify if these three mutations are real or not:
a) The quality of the reads is good: MAPQ between 60 and 29.
b) The variants are supported by reads from both strands.
c) There are no germline mutations annotated in dbSNP, 1000 genomes, etc.
d) Blat scores for the supporting reads in other regions of the genome are lower than 300, while the scores for this region are higher than 900.
But as I said before, I think that the fact that they are on the same reads is not a good signal.
Do you think that these could be false mutations? or real mutations from another region of the genome?
Thanks in advance.