VarDict Raw Output

In a single sample mode, VarDict’s raw output consists of 34 columns. Below are information on those 34 columns:

Column No	Column Name	Desc
1	Sample	Name of sample
2	Gene	Gene symbol or 4th column in BED file
3	Chr	Chromosome
4	Start	Start position
5	End	End position
6	Ref	Reference allele sequence
7	Alt	Alternative allele sequence
8	Depth	Total coverage
9	AltDepth	No. of reads supporting alternative allele
10	RefFwdReads	No. of reads in forward orientation supporting reference allele
11	RefRevReads	No. of reads in reverse orientation supporting reference allele
12	AltFwdReads	No. of reads in forward orientation supporting alternative allele
13	AltRevReads	No. of reads in reverse orientation supporting alternative allele
14	Genotype	Genotype (deprecated and can be erroneous. It’s not carried into VCF)
15	AF	Allele frequency in fraction [0-1]
16	Bias	Whether there’s strand bias. It consists two numbers. First number is for reference allele. 2nd number is for alternative allele. Numbers are 0-2. 0 means not enough to determine bias. 1 means only one orientation observed. 2 means both orientations observed. 2:1 would indicate strand bias, but not 1:1.
17	PMean	The mean position in reads of alternative allele. Smaller number would suggest false positives.
18	PStd	Indicate whether the position in reads are the same. 0 means they are the same, 1 mean they are different.
19	QMean	The mean base quality for alternative allele.
20	QStd	Indicate whether the base quality in reads are the same. 0 means they are the same, 1 mean they are different.
21	MQ	The mean mapping quality for reads supporting alternative allele.
22	Sig_Noise	Signal to noise ratio. The higher the number (>1.5), the more reliable the calls.
23	HiAF	Allele frequency if only high base quality reads are used.
24	ExtraAF	Extra allele frequency recovered from local realignment.
25	shift3	No. of bases the Indel can be shifted 3’ with equivalent alignment.
26	MSI	Whether there’s microsatellite in sequence context
27	MSI_NT	Number of bp per unit for MSI. 1 would indicate homopolymer, 2 for di-nucleotide repeat, and so on…
28	NM	Mean number of mismatches in the reads (excluding indels) supporting alternative allele
29	HiCnt	No. of reads with high base quality
30	HiCov	No. of coverage with high base quality
31	5pFlankSeq	20bp flanking the variants at 5’
32	3pFlankSeq	20bp flanking the variants at 3’
33	Seg	The genomic segment variant is called
34	VarType	The type of variants. Values are: SNV, MNV, Insertion, Deletion, and Complex