I know in exome sequencing, CG content of exons effect on the result, especially in exon number 1 usually GC content is higher than the other exons.
The question is: In exome sequence filtering is there any cut off/threshold related to GC content around a variant position? For example +/- 20 bp around a variant position.
GC content affects the ability to capture and sequence a region with high and low GC content being more difficult to sequence (get good coverage). I do not know of folks using GC cutoffs for variant positions. I'd suggest looking into using variant quality score recalibration for accounting for the various biases that affect variant quality.
thanks Sean, I know it effects on exome capturing.Indeed I have an excel file with a lot of column.There is no header named VQSR in my file.So I do not know how can I check biases that affect on variant quality.In addition to CG I have the same problem with some other headers like MQ0, MQ0fraction,SB and BaseQualityRankSumTest. I would greatly appreciate if answer these question. But according to your answer if I use variant quality score recalibration, I do not need to check all qualities.Is it right? How can I use variant quality score recalibration?
Dear Sean, I saw the webpage and also asked about VQSR.They told me we can not do VQSR for small sample size.My sample size was 20 and normally in this situation people works based on read depth and phred score.I would greatly appreciate if I have your comment.Is the any solution?
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version 2.3.6
what is CG? Can you edit your question to fix it.
I was assuming that CG content was the same as GC content, but I agree that this could be a misunderstanding.