# HG changeset patch # User bcrain-completegenomics # Date 1339522016 14400 # Node ID 4851ac12f70439b7557b4d8db83ef0b8fb0d6104 # Parent 63541ee5f3192d63f0fddd22c4f65c459f7a2663 Uploaded diff -r 63541ee5f319 -r 4851ac12f704 listtestvariants.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/listtestvariants.xml Tue Jun 12 13:26:56 2012 -0400 @@ -0,0 +1,239 @@ + + + + + + + cgatools + + + + cgatools listvariants + --beta + --reference ${crr.fields.path} + --output $output1 + #if $include_list.listing == "yes" + --variant-listing $include_list.list + #end if + $longvar + --variants + #if $file_types.data_sources.data_source == "in" + #for $v in $file_types.data_sources.varfiles + ${v.input} + #end for + #else + `cat $file_types.data_sources.varlist` + #end if + ; + + cgatools testvariants + --beta + --reference ${crr.fields.path} + --output $output2 + --input $output1 + --variants + #if $file_types.data_sources.data_source == "in" + #for $v in $file_types.data_sources.varfiles + ${v.input} + #end for + #else + `cat $file_types.data_sources.varlist` + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants. + +cgatools: http://sourceforge.net/projects/cgatools/files/ + +----- + +**cgatools Manual**:: + + COMMAND NAME + listvariants - Lists the variants present in a variant file. + + DESCRIPTION + Lists all called variants present in the specified variant files, in a + format suitable for processing by the testvariants command. The output is a + tab-delimited file consisting of the following columns: + + variantId Sequential id assigned to each variant. + chromosome The chromosome of the variant. + begin 0-based reference offset of the beginning of the variant. + end 0-based reference offset of the end of the variant. + varType The varType as extracted from the variant file. + reference The reference sequence. + alleleSeq The variant allele sequence as extracted from the variant + file. + xRef The xRef as extrated from the variant file. + + OPTIONS + -h [ --help ] + Print this help message. + + --beta + This is a beta command. To run this command, you must pass the --beta + flag. + + --reference arg + The reference crr file. + + --output arg (=STDOUT) + The output file (may be omitted for stdout). + + --variants arg + The input variant files (may be positional args). + + --variant-listing arg + The output of another listvariants run, to be merged in to produce the + output of this run. + + --list-long-variants + In addition to listing short variants, list longer variants as well + (10's of bases) by concatenating nearby calls. + + SUPPORTED FORMAT_VERSION + 0.3 or later + + + + COMMAND NAME + testvariants - Tests variant files for presence of variants. + + DESCRIPTION + Tests variant files for presence of variants. The output is a tab-delimited + file consisting of the columns of the input variants file, plus a column + for each assembly results file that contains a character code for each + allele. The character codes have meaning as follows: + + 0 This allele of this genome is consistent with the reference at this + locus but inconsistent with the variant. + 1 This allele of this genome has the input variant at this locus. + N This allele of this genome has no-calls but is consistent with the + input variant. + + OPTIONS + -h [ --help ] + Print this help message. + + --beta + This is a beta command. To run this command, you must pass the --beta + flag. + + --reference arg + The reference crr file. + + --input arg (=STDIN) + The input variants to test for. + + --output arg (=STDOUT) + The output file (may be omitted for stdout). + + --variants arg + The input variant files (may be passed in as arguments at the end of + the command). + + SUPPORTED FORMAT_VERSION + 0.3 or later + +