how to filter at the information of DP(read depth at this position for this sample (Integer))

Question

[897598644]

By far, I have call variants and will confirm the site using sanger.

How should II choose DP(read depth at this position for this sample (Integer)) cutoff ? It will be better to give the references of that value.

Thx in advance!

[Coryza]

I don't understand your question completely. Related to DP; You could choose your cut-off based on the sequencing depth.

[897598644]

so what is the rule?

[Devon Ryan]

There is no rule. The best you can do is use your best judgement given the underlying depth distribution.

[iraun]

I don't understand very well your question but, you can set DP cutoff depending on global coverage of your bam.

[897598644]

so what is the rule?

[Ashutosh Pandey]

Your question is unclear. Do you want to filter your SNPs and Indels based on read depth before using Sanger sequencing to validate them? If this is your question then read some papers that have resequenced genomes (similar to what you have been working on) and have identified SNPs and indels. We resequence different mice strains and I prefer using 5 reads with alternative allele to call for SNP or indel. Some people use 3 minimum supporting reads for SNPs and 5 for indels. It varies.