Vdb Field In Samtools
3
3
Entering edit mode
10.0 years ago

samtools VCF files has a field "VDB" which I believe is "Variant Distance Bias".

Does someone know exactly what this is and how to interpret this field? Can these be both negative and positive? I.e. what does high/low value for VDB mean?

Here are two examples from my VCF file.

DP=64;VDB=0.0398;AF1=1;AC1=4;DP4=0,0,9,48;MQ=44;FQ=-112

DP=447;VDB=0.0419;AF1=1;AC1=4;DP4=0,1,119,288;MQ=47;FQ=-286;PV4=1,0.12,0.32,1

Thanks a bunch!

samtools • 8.5k views
ADD COMMENT
4
Entering edit mode
9.6 years ago
pd3 ▴ 340

VDB (variant distance bias) checks if variant bases occur at random positions in the aligned portion of the reads. It is useful mainly for RNA-seq reads which are aligned against a genomic reference sequence. Higher values indicate higher likelihoods that the variant is distributed within the reads randomly.

ADD COMMENT
1
Entering edit mode
10.0 years ago

One response at http://seqanswers.com/forums/showthread.php?t=14582 guesses that the VDB field indicates a potential misalignment due to a nearby SNP.

The following from VCF Tools @ Sourceforge,net seems to agree: The "end distance alignment" tests if variant bases tend to occur at a fixed distance from the end of reads, which is usually an indication of misalignment.

ADD COMMENT
0
Entering edit mode

Thansk for the links.

So higher values indicate greater bias and should be flagged as "suspicious"? Or is it the other way around i.e. lower values should be discarded? Thanks a lot!

ADD REPLY
0
Entering edit mode
8.6 years ago
Marina Manrique ★ 1.3k

A brief description of all the flags present in the INFO and FORMAT fields of the VCF file can be found in the first lines of the file (which start by ##)

##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
ADD COMMENT

Login before adding your answer.

Traffic: 1800 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6