# HG changeset patch # User devteam # Date 1473969816 14400 # Node ID eac1f91d50b16ef3db8d866b73499f6051bf5abc # Parent b71701c8b88441b86723606bd03d7c2e8eca0253 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcffilter commit 0b9b6512272b82637c2f1e831367e89aed77ae79 diff -r b71701c8b884 -r eac1f91d50b1 macros.xml --- a/macros.xml Mon Nov 09 12:31:38 2015 -0500 +++ b/macros.xml Thu Sep 15 16:03:36 2016 -0400 @@ -1,7 +1,7 @@ - vcflib + vcflib @@ -10,6 +10,7 @@ + 1.0.0_rc1 diff -r b71701c8b884 -r eac1f91d50b1 tool_dependencies.xml --- a/tool_dependencies.xml Mon Nov 09 12:31:38 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - - diff -r b71701c8b884 -r eac1f91d50b1 vcffilter.xml --- a/vcffilter.xml Mon Nov 09 12:31:38 2015 -0500 +++ b/vcffilter.xml Thu Sep 15 16:03:36 2016 -0400 @@ -1,78 +1,77 @@ - - filter VCF data in a variety of attributes - - macros.xml - - - tabix - - - - - ln -s "${input1}" input1.vcf && - bgzip input1.vcf && - tabix -p vcf input1.vcf.gz && - vcffilter ${filterList} input1.vcf.gz > "${out_file1}" - - - - - - - - - - - - - - - - - - - - - - - - - - - - -You can specify the following options within the **Specify filtering expression** box in any combination:: - - -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter - -g, --genotype-filter specifies a filter to apply to the genotype fields of records - -s, --filter-sites filter entire records, not just alleles - -t, --tag-pass tag vcf records as positively filtered with this tag, print all records - -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records - -A, --append-filter append the existing filter tag, don't just replace it - -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 - -Any number of filters may be specified. They are combined via logical AND unless the --or option is specified. 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, & - - -To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: - - -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_PART_OF_VCFLIB@ - - - + + filter VCF data in a variety of attributes + + macros.xml + + + htslib + tabix + + + + + ln -s "${input1}" input1.vcf && + bgzip input1.vcf && + tabix -p vcf input1.vcf.gz && + vcffilter ${filterList} input1.vcf.gz > "${out_file1}" + + + + + + + + + + + + + + + + + + + + + + + + + + +You can specify the following options within the **Specify filtering expression** box in any combination:: + + -f, --info-filter specifies a filter to apply to the info fields of records, removes alleles which do not pass the filter + -g, --genotype-filter specifies a filter to apply to the genotype fields of records + -s, --filter-sites filter entire records, not just alleles + -t, --tag-pass tag vcf records as positively filtered with this tag, print all records + -F, --tag-fail tag vcf records as negatively filtered with this tag, print all records + -A, --append-filter append the existing filter tag, don't just replace it + -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 + +Any number of filters may be specified. They are combined via logical AND unless the --or option is specified. 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, & + + +To restrict output to a specific location use the -r option (must be used in conjunction with -g or -f):: + + -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_PART_OF_VCFLIB@ + + +