vcf-annotate1
Annotate vcf file, add filters or custom annotations
Usage
cat {in.vcf | vcf-annotate
[OPTIONS]
>
out.vcf}
Overview
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
-aannotations.gz-ddescriptions.txt | bgzip-c>out.vcf.gz zcat in.vcf.gz | vcf-annotate-f+/-a/c=3,10/q=3/d=5/-D-aannotations.gz-ddescriptions.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'
Releases
Unchanged in 7 releases since Debian 7 (Wheezy).