Mercurial > repos > anton > vcffilter
changeset 2:77e44d465705 draft
Uploaded
| author | anton |
|---|---|
| date | Mon, 12 May 2014 16:32:03 -0400 |
| parents | e5dd21db760b |
| children | 6c2640e8ecbb |
| files | vcffilter.xml |
| diffstat | 1 files changed, 14 insertions(+), 7 deletions(-) [+] |
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--- a/vcffilter.xml Mon May 12 15:53:18 2014 -0400 +++ b/vcffilter.xml Mon May 12 16:32:03 2014 -0400 @@ -50,20 +50,27 @@ -a, --allele-tag apply -t on a per-allele basis. adds or sets the corresponding INFO field tag -v, --invert inverts the filter, e.g. grep -v -o, --or use logical OR instead of AND to combine filters + -r, --region specify a region on which to target the filtering (must be used in conjunction with -f or -g Filters are specified in the form {ID} {operator} {value}:: - -f "DP > 10" # for info fields - -g "GT = 1|1" # for genotype fields - -f "CpG" # for 'flag' fields + -f "DP > 10" # for info fields + -g "GT = 1|1" # for genotype fields + -f "CpG" # for 'flag' fields + +Any number of filters may be specified. They are combined via logical AND unless --or is specified on the command line. For convenience, you can specify "QUAL" to refer to the quality of the site, even though it does not appear in the INFO fields. Operators can be any of: =, !, <, >, pipe, & -Any number of filters may be specified. They are combined via logical AND -unless --or is specified on the command line. + +To restrict output to a specific location use -r option (much be used in conjunction with -g or -f):: -For convenience, you can specify "QUAL" to refer to the quality of the site, even -though it does not appear in the INFO fields. + -r chr20:14000-15000 # only output calls between positions 14,000 and 15,000 on chromosome 20 + -r chrX # only output call on chromosome X + +----- + +Vcffilter is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). </help> </tool>