I'm working with 70 samples of whole genome data (the whole genome of 70 individuals). I'm returning to the field after some time away from my academic training, and I don't have a lot of experience with whole genome data from which to draw comparisons. At this time, I dont have any demographic info about the samples.
I've been provided with BAM files, against which samtools mpileupand bcftools call has been run. Then the BCF files were bcftools merge-ed into one large file of 70 samples.
I'm currently working on validating the SNPs in the BCF files. One interesting data curve I've noticed is the Allele-frequency/number-of-SNPs.
So this is the AF on the X, and number of SNPs at this AF on Y. The "jump point" is at AF=0.49...so basically, where the SNPs go from hetero- to homozygous.
I would intuitively expect (in a random population) that this curve would be closer to a bell curve...or at least more randomly distributed. And yet this is quite the opposite.
I'm also curious if the Ti/Tv ratio is significant...as there's a spike at the same place, and I wouldn't expect to see the ratio change amongst SNPs at all (should I?)
0 answers
No answers yet.
Log in to answer this question.
-
Vcf Filtering
written by Marc Ibanez •
-
number of heterozygous and homozygous SNPs across lineages
written by romain.derelle •
-
Reference TiTv ratio for mouse WGS?
written by serpalma.v •
-
Using synonymous vs. non-synonymous ALT for SNP data validation
written by rightmirem •
-
Recreating a Genomic reference (.fastq) from a BCF file
written by rightmirem •
-
Unusual reports from "bcftools stats" (making me question my data)
written by rightmirem •
-
How to validate the OVERALL quality of a VCF/BCF file (Data munging)
written by rightmirem •
-
Ti Tv ratio and their usefulness in exome sequencing
written by mangfu100
-
vcftools and SnpSift give different values for Ts/Tv ratio
written by ethan.kaufman
-
Writing Script That Compares Results From Multiple Sample Snp Callers By Calculating Ti/Tv Ratio
written by mubozhi •
Could you add axes labels also on the plots shown, to help readers?
Did you set missing genotypes to ref (-0) when using bcftools merge?
Hello, yes, the spike at 0.49 is unusual for a multi-sample VCF/BCF, but it could be explained if, when you merged your samples, the AF field was not updated by BCFtools. Did your colleagues split multi-allelic sites and left-align indels prior to merging?
I would fully expect, however, a binary distribution for AF (0.5 or 1.0) if I was analysing a single-sample VCF. If you have a single-sample VCF, then your AF should be either 0.5 (heterozygous with AC=1) or 1.0 (homozygous with AC=2). If you then merge this with another sample that does not contain the same variant, then you will get the following:
The phenomenon that you see may in addition be related to sample population. You have not mentioned from where they are based. If it's a community that has not mixed (genetically) with other groups of people for geographical, religious, ethnic, or other reason, then I would fully expect a skewed AF distribution.