Indel treated as SNP through mapping with Indel
cmarques2000 opened this issue · comments
Hello. Im a Master degree student with the objective of detecting RNA variants. Ive done the analysis of the DNA/exome and currently I'm trying to confirm what i found in the DNA/exome on the RNA reads.
I've been running STAR(on Galaxy) with different parameters but every single result is the same.
I also did the mapping with Bowtie2 on Galaxy and i compared with the bam file from STAR and i find some mismatches.
My current pipeline for my work is all in Galaxy Project.
I need an opinion for what are the best parameters so STAR doesn't consider Indels as SNPs using hg19 as reference genome.
