Hi guys,
I am working on some exome datasets and ran into a problem:
Is there already a published way of looking at sites which should have been captured but didn't be sequenced?
E.g. we did exome sequencing of a patient and I did alignment, SNP calling (GATK) and afterwards variant annotation using Annovar. We are now down to 3 SNPs. While we are now trying to validate that experimentally I was wondering how to determine parts of the exome which are not covered by let's assume 20+ reads. Moreover, how could one determine homozygote exon deletions (they should not be covered by sequences at all, but that can happen due to chance as well)?
Any help appreciated,
Peter
I am working on some exome datasets and ran into a problem:
Is there already a published way of looking at sites which should have been captured but didn't be sequenced?
E.g. we did exome sequencing of a patient and I did alignment, SNP calling (GATK) and afterwards variant annotation using Annovar. We are now down to 3 SNPs. While we are now trying to validate that experimentally I was wondering how to determine parts of the exome which are not covered by let's assume 20+ reads. Moreover, how could one determine homozygote exon deletions (they should not be covered by sequences at all, but that can happen due to chance as well)?
Any help appreciated,
Peter
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