Mercurial > repos > iuc > bcftools_query

comparison bcftools_query.xml @ 5:ecc6b09ed3a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
author iuc
date Thu, 13 Apr 2017 16:26:56 -0400
parents 19e871cd19ab
children 8e464dda9ad5
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4:19e871cd19ab 5:ecc6b09ed3a8
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@ 11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILES@ 12 @PREPARE_INPUT_FILES@
13 #set $section = $sec_restrict 13 #set $section = $sec_restrict
14 @PREPARE_TARGETS_FILE@ 14 @PREPARE_TARGETS_FILE@
15 @PREPARE_REGIONS_FILE@
15 16
16 bcftools @EXECUTABLE@ 17 bcftools @EXECUTABLE@
17 18
18 ## Query section 19 ## Query section
19 #set $section = $sec_query 20 #set $section = $sec_query
98 ``%MASK`` Indicates presence of the site in other files (with multiple files) 99 ``%MASK`` Indicates presence of the site in other files (with multiple files)
99 ``%TAG{INT}`` Curly brackets to subscript vectors (0-based) 100 ``%TAG{INT}`` Curly brackets to subscript vectors (0-based)
100 ``%FIRST_ALT`` Alias for %ALT{0} 101 ``%FIRST_ALT`` Alias for %ALT{0}
101 ``[]`` The brackets loop over all samples 102 ``[]`` The brackets loop over all samples
102 ``%GT`` Genotype (e.g. 0/1) 103 ``%GT`` Genotype (e.g. 0/1)
104 ``%TBCSQ`` Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
103 ``%TGT`` Translated genotype (e.g. C/A) 105 ``%TGT`` Translated genotype (e.g. C/A)
104 ``%IUPACGT`` Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A) 106 ``%IUPACGT`` Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
105 ``%LINE`` Prints the whole line 107 ``%LINE`` Prints the whole line
106 ``%SAMPLE`` Sample name 108 ``%SAMPLE`` Sample name
109 ``%POS0`` POS in 0-based coordinates
110 ``%END`` End position of the REF allele
111 ``%END0`` End position of the REF allele in 0-based cordinates
112 ``\n`` new line
113 ``\t`` tab character
114
107 115
108 Examples: 116 Examples:
109 117
110 :: 118 ::
111 119
112 ``bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz`` 120 # Print chromosome, position, ref allele and the first alternate allele
113 ``bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz`` 121 bcftools query -f '%CHROM %POS %REF %ALT{0}\n' file.vcf.gz
122
123 # Similar to above, but use tabs instead of spaces, add sample name and genotype
124 bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz
125
126 # Print FORMAT/GT fields followed by FORMAT/GT fields
127 bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf
128
129 # Make a BED file: chr, pos (0-based), end pos (1-based), id
130 bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf
131
114 132
115 @COLLAPSE_HELP@ 133 @COLLAPSE_HELP@
116 @REGIONS_HELP@ 134 @REGIONS_HELP@
117 @TARGETS_HELP@ 135 @TARGETS_HELP@
118 @EXPRESSIONS_HELP@ 136 @EXPRESSIONS_HELP@