vcf-annotate: Annotate vcf file, add filters or custom annotations

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.

+: 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]

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

key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'