To filter exome sequence data and remove false positive I know read depth and Phred score are routinely applied.
But there are following items (related to quality) which I would like to know is there any threshold/cut off for them? and In which step of filtration strategy I should apply them(at the beginning or at the end)?
GC = GC content within 20 bp +/- the variant
HRun = Largest Contiguous Homopolymer Run of Variant Allele In Either Direction
HW = Phred-scaled p-value for Hardy-Weinberg violation. Extreme variations on heterozygous calls indicate a false positive call
MQ0
MQ0Fraction = RMS (Root Mean Square, also known as quadratic mean) Mapping Quality. Regions of excessively low mapping quality are ambiguously mapped and variants called within are suspicious
SB = Strand Bias
BaseQualityRankSumTest = The u-based z-approximation from the Mann-Whitney Rank Sum Test for base qualities (ref bases vs.bases of the alternate allele).
2 answers
I would suggest taking a look at variant quality score recalibration.
To add to Sean Davis answer Broad has a nice description of their "best practice" for variant detection here: http://www.broadinstitute.org/gatk/guide/topic?name=best-practices (I'm guessing that will want to do something like that) This approach is if particular interest if you are planing to use one of their variant callers, the UnifiedGenotyper, of the new HaplotypeCaller.
I'm not sure that you need a hard threshold - the VQSR should create a model from the data. Quoting from the link above: "The tool used here is the Variant quality score recalibrator which builds an adaptive error model using known variant sites and then applies this model to estimate the probability that each variant in the callset is a true genetic variant or a machine/alignment artifact. All filtering criteria are learned from the data itself."
VQSR allows you to avoid having to make such arbitrary cutoffs by modeling errors in the data. There is no need (or should you desire) to define cutoffs based on single parameters.
Log in to answer this question.
-
bcftools mpileup returns vcf files with only headers
written by Brenden •
-
Optimising False Positive Detection in NGS Pipelines Using Mapping and Base Quality Scores
written by ManuelDB
-
Liftedover vcf header/contig compatibility
written by LayneSadler
-
How to insert quotes around description of format field in vcf header?
written by Alewa
-
Weird behavior of `--max-depth` argument from `bcftools mpileup` command when its value is too low
written by sbstevenlee •
-
What are the range or ceiling of metrics like DP4 , MQP, etc to filter variants?
written by Dayna •
-
VCF/BCF File format QS score in INFO header
written by ga32huv •
-
GATK variant recal malformed vcf
written by SemiQuant
-
samtools/bcftools strange (error ?) lack of call
written by mbourgey •
-
Filtering Strategy In Exome Sequencing And Quality Control
written by Omid
Please stop duplicating posts - you have already asked this here:
http://www.biostars.org/post/show/49453/filtering-strategy-in-exome-sequencing-and-quality-control/
and on SeqAnswers as well.