vcf-compare(1) [debian man page]
VCF-COMPARE(1) User Commands VCF-COMPARE(1) NAME
vcf-compare - compare bgzipped and tabix indexed VCF files SYNOPSIS
compare-vcf [OPTIONS] file1.vcf file2.vcf ... DESCRIPTION
About: Compare bgzipped and tabix indexed VCF files. (E.g. bgzip file.vcf; tabix -p vcf file.vcf.gz) OPTIONS
-c, --chromosomes <list|file> Same as -r, left for backward compatibility. Please do not use as it will be dropped in the future. -d, --debug Debugging information. Giving the option multiple times increases verbosity -H, --cmp-haplotypes Compare haplotypes, not only positions -m, --name-mapping <list|file> Use with -H when comparing files with differing column names. The argument to this options is a comma-separated list or one mapping per line in a file. The names are colon separated and must appear in the same order as the files on the command line. -R, --refseq <file> Compare the actual sequence, not just positions. Use with -w to compare indels. -r, --regions <list|file> Process the given regions (comma-separated list or one region per line in a file). -s, --samples <list> Process only the listed samples. Excluding unwanted samples may increase performance considerably. -w, --win <int> In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a SNP or an indel). -h, -?, --help This help message. vcf-compare 0.1.5 July 2011 VCF-COMPARE(1)
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VCF-ANNOTATE(1) User Commands VCF-ANNOTATE(1) 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 FROM[ TO][ VALUE]+. -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' vcf-annotate 0.1.5 July 2011 VCF-ANNOTATE(1)