identifying mutation & copy numbers using sequencing data

Question

[ashkan]

I am looking for mutation and copy numbers. do you guys know what type of sequencing data can be used to get such data?

[WouterDeCoster]

This question could use more information. Do you want to discover mutations or resequence those? Genome-wide or in a locus? Does "mutation & copy numbers" mean copy number variants and SNPs too? Which is the organism you are working on? Which is the size of the CNVs you aim to sequence? In how many samples?

Answer 1

[Vivek]

If you have the budget for whole genome sequencing, that would be top choice. Otherwise exomes would be fine as long as your CNVs of interest are expected to be included in targeted capture regions.

[WouterDeCoster]

exomes would be fine

CNV detection based on WES is noisy at best and not an optimal approach based on limited experience and literature... Do you have a better experience with this? Would be interested to hear about which tools you used.

[Vivek]

I was mentioning more in the sense of genotyping known cnvs where you have phenotypes being identified with a deletion in one chromosome plus a damaging SNP on the other. If novel cnvs are your target then yeah wgs is your best and probably only option.

[WouterDeCoster]

Right, makes sense and I fully agree. WGS with long reads (PacBio, Nanopore), Illumina mate pairs or large insert library, or perhaps even BioNano Genomics optical scaffolding. Presumably best detection with a combination of technologies.