Man page - vcf-annotate(1)
Packages contains this manual
- vcf-query(1)
- vcf-stats(1)
- vcf-to-tab(1)
- vcf-concat(1)
- vcf-sort(1)
- vcf-indel-stats(1)
- vcf-phased-join(1)
- fill-aa(1)
- vcf-isec(1)
- vcf-consensus(1)
- vcf-tstv(1)
- vcf-merge(1)
- vcf-subset(1)
- vcf-contrast(1)
- vcf-fix-newlines(1)
- fill-an-ac(1)
- vcftools(1)
- vcf-validator(1)
- fill-fs(1)
- vcf-fix-ploidy(1)
- vcf-compare(1)
- fill-ref-md5(1)
- vcf-annotate(1)
- vcf-convert(1)
- vcf-shuffle-cols(1)
apt-get install vcftools
Manual
VCF-ANNOTATE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
Filters:
Example:
Where descriptions.txt contains:
NAME
vcf-annotate - annotate VCF file, add filters or custom annotations
SYNOPSIS
cat in.vcf | vcf-annotate [ OPTIONS ] > out.vcf
DESCRIPTION
About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.
Currently annotates only the INFO column, but it will be extended on demand.
OPTIONS
-a , --annotations <file.gz>
The tabix indexed file with the annotations: CHR\tFROM[\tTO][\tVALUE]+.
-c , --columns <list>
The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third column should be ignored. If TO is not present, it is assumed that TO equals to FROM.
-d , --description <file|string>
Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description=’HapMap2 membership’. The descriptions can be read from a file, one annotation per line.
-f , --filter <list>
Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.
-h , -?, --help
This help message.
Filters:
|
+ |
Apply all filters with default values (can be overridden, see the example below). |
||
|
-X |
Exclude the filter X |
1, StrandBias
FLOAT Min P-value for strand bias (given PV4) [0.0001]
2, BaseQualBias
FLOAT Min P-value for baseQ bias [1e-100]
3, MapQualBias
FLOAT Min P-value for mapQ bias [0]
4, EndDistBias
FLOAT Min P-value for end distance bias [0.0001]
a, MinAB
INT Minimum number of alternate bases [2]
c, SnpCluster
INT1,INT2 Filters clusters of ’INT1’ or more SNPs within a run of ’INT2’ bases []
D, MaxDP
INT Maximum read depth [10000000]
d, MinDP
INT Minimum read depth [2]
q, MinMQ
INT Minimum RMS mapping quality for SNPs [10]
Q, Qual
INT Minimum value of the QUAL field [10]
r, RefN
Reference base is N []
W, GapWin
INT Window size for filtering adjacent gaps [10]
w, SnpGap
INT SNP within INT bp around a gap to be filtered [10]
Example:
zcat in.vcf.gz | vcf-annotate -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f +/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz
Where descriptions.txt contains:
key=INFO,ID=GN,Number=1,Type=String,Description=’Gene Name’ key=INFO,ID=STR,Number=1,Type=Integer,Description=’Strand’