Hi all,
I am working with some exome sequencing data. I have done the mapping, pileup, filtering and variant calling. After all that... my data look weird, I am getting A LOT of homozygous calls and when annotating most of them are not in dbSNP. These things make me suspicious about my data. Also, I checked a few of the heterozygous SNPs and 1/10 was actually heterozygous.
Does anyone have any idea of what might be wrong with my data??? Is there a way to check if the sequencing actually worked, besides relying on the Phred-like scores???
Thank you!
I am working with some exome sequencing data. I have done the mapping, pileup, filtering and variant calling. After all that... my data look weird, I am getting A LOT of homozygous calls and when annotating most of them are not in dbSNP. These things make me suspicious about my data. Also, I checked a few of the heterozygous SNPs and 1/10 was actually heterozygous.
Does anyone have any idea of what might be wrong with my data??? Is there a way to check if the sequencing actually worked, besides relying on the Phred-like scores???
Thank you!
Comment