diff bcftools_query.xml @ 5:24ff7b989329 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e

--- a/bcftools_query.xml	Sat Mar 11 18:04:22 2017 -0500
+++ b/bcftools_query.xml	Thu Apr 13 17:45:03 2017 -0400
@@ -12,6 +12,7 @@
 @PREPARE_INPUT_FILES@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
 
 bcftools @EXECUTABLE@
 
@@ -100,17 +101,34 @@
     ``%FIRST_ALT``      Alias for %ALT{0}
     ``[]``              The brackets loop over all samples
     ``%GT``             Genotype (e.g. 0/1)
+    ``%TBCSQ``          Translated FORMAT/BCSQ. See the csq command above for explanation and examples.
     ``%TGT``            Translated genotype (e.g. C/A)
     ``%IUPACGT``        Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
     ``%LINE``           Prints the whole line
     ``%SAMPLE``         Sample name
+    ``%POS0``           POS in 0-based coordinates
+    ``%END``            End position of the REF allele
+    ``%END0``           End position of the REF allele in 0-based cordinates
+    ``\n``              new line
+    ``\t``              tab character
+
 
   Examples:
 
   ::
 
-    ``bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz``
-    ``bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz``
+    # Print chromosome, position, ref allele and the first alternate allele
+    bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz
+
+    # Similar to above, but use tabs instead of spaces, add sample name and genotype
+    bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz
+
+    # Print FORMAT/GT fields followed by FORMAT/GT fields
+    bcftools query -f 'GQ:[ %GQ] \t GT:[ %GT]\n' file.vcf
+
+    # Make a BED file: chr, pos (0-based), end pos (1-based), id
+    bcftools query -f'%CHROM\t%POS0\t%END\t%ID\n' file.bcf
+
 
 @COLLAPSE_HELP@
 @REGIONS_HELP@