Question: coverage of a SNP site?
0
gravatar for Susmita Mandal
5 weeks ago by
Bangalore
Susmita Mandal0 wrote:

Hey all,

I have a doubt regarding what does it mean coverage at SNP sites. I'm supposed to be finding genes with SNPs ≥ 10X coverage in the samples and also they have taken average 8 SNPs/ transcripts. Any idea what it could mean.

Thanks

Susmita

snp coverage ase ngs bedtools • 159 views
ADD COMMENTlink modified 5 weeks ago by Kevin Blighe33k • written 5 weeks ago by Susmita Mandal0

Can you specify the context?

ADD REPLYlink written 5 weeks ago by gab20
3
gravatar for cpad0112
5 weeks ago by
cpad011210k
India
cpad011210k wrote:
  1. call the variants
  2. Filter the variants with read depth > 10
  3. Identify the genes that house the variants from step 2
  4. Count the variants per gene
  5. Filter the genes with more than 8 SNPs

You can further refine the quest by annotating the vcf. Annotate VCF, filter variants with more than 10x read depth, if you have sufficient number of variants post filtering, filter the variants further by effect (non-synonymous), then filter by number of variants per gene.

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by cpad011210k

Thank you so much. Now i get it :)

ADD REPLYlink written 5 weeks ago by Susmita Mandal0
1
gravatar for Kevin Blighe
5 weeks ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k wrote:

'Coverage' and 'read depth' are commonly mis-used. Read depth is the number of reads that align to any given base position. Coverage ('depth of coverage') is a summary metric that says that all bases in a particular region (or regions) achieved a minimum read depth. For example, we may say that 99% of our target regions achieved > 10x coverage, meaning that 99% of bases had an individual read-depth > 10. We may also say that we performed whole genome sequencing with a target depth of coverage of 5x, meaning that we provided sufficient re-agents and ran a sufficient number of sequencing cycles such that the expectation is that each base, genome-wide, will have a read-depth >= 5.

Your wording is confusing, but you could likely interpret it as that you are expected to filter your data to include only those SNPs that have read depth > 10.

Kevin

ADD COMMENTlink written 5 weeks ago by Kevin Blighe33k
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