| Next changeset 1:f75bf16ac901 (2023-01-22) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beagle commit ccb3f8eaa99490f8513200e45fc59e5011fb41e8" |
|
added:
beagle.xml macros.xml test-data/plink.map test-data/ref.bref3 test-data/ref.vcf.gz test-data/target.vcf.gz test-data/test.vcf.gz test-data/test_output.log test-data/test_output.vcf |
| b |
| diff -r 000000000000 -r 553b27c30eb8 beagle.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/beagle.xml Sat Jul 03 23:33:37 2021 +0000 |
| [ |
| b'@@ -0,0 +1,314 @@\n+<tool id=\'beagle\' name=\'Beagle\' version=\'@TOOL_VERSION@+galaxy@SUFFIX_VERSION@\' profile=\'20.01\'>\n+ <description>phasing genotypes and imputing ungenotyped markers</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro=\'edam_ontology\' />\n+ <expand macro=\'requirements\' />\n+ <command detect_errors=\'exit_code\'><![CDATA[\n+ #set out_prefix=\'out\'\n+ #if $optional_inputs.ref.ext == \'bref3\'\n+ ln -s \'${optional_inputs.ref}\' ref.bref3 &&\n+ #end if\n+ beagle\n+ gt=\'${gt}\'\n+ #if $optional_inputs.ref and $optional_inputs.ref.ext == \'bref3\'\n+ ref=ref.bref3\n+ #else if $optional_inputs.ref\n+ ref=\'${optional_inputs.ref}\'\n+ #end if\n+ #if $optional_inputs.map\n+ map=\'${optional_inputs.map}\'\n+ #end if\n+ #if $chrom\n+ chrom=\'${chrom}\'\n+ #end if\n+ #if $optional_inputs.excludesamples\n+ excludesamples=\'${optional_inputs.excludesamples}\'\n+ #end if\n+ #if $optional_inputs.excludemarkers\n+ excludemarkers=\'${optional_inputs.excludemarkers}\'\n+ #end if\n+ ne=$ne\n+ window=$window\n+ overlap=$overlap\n+ #if $seed\n+ seed=$seed\n+ #end if\n+ #if $err\n+ err=$err\n+ #end if\n+ burnin=$phasing_parameters.burnin\n+ iterations=$phasing_parameters.iterations\n+ phase-states=$phasing_parameters.phase_states\n+ impute=$imputation_parameters.impute\n+ imp-states=$imputation_parameters.imp_states\n+ imp-segment=$imputation_parameters.imp_segment\n+ imp-step=$imputation_parameters.imp_step\n+ cluster=$imputation_parameters.cluster\n+ ap=$imputation_parameters.ap\n+ gp=$imputation_parameters.gp\n+ out=$out_prefix\n+ nthreads=\\${GALAXY_SLOTS:-1}\n+ && gunzip \'out.vcf.gz\'\n+ ]]> </command>\n+ <inputs>\n+ <param argument="gt" type="data" format="vcf" label="VCF file" \n+ help="It specifies a VCF file containing genotypes for the study samples. \n+ Each VCF record must contain a GT (genotype) format field"/>\n+ <section name="optional_inputs" title="Optional input files" expanded="true">\n+ <param argument="ref" type="data" format="vcf,bref3" optional="true" label="Bref3 or VCF file with phased genotypes" \n+ help="Each genotype must have two phased, non-missing alleles. If a VCF file is specified, the \n+ phased allele separator must be used \'|\'"/>\n+ <param argument="map" type="data" format="txt" optional="true" label="PLINK map file with cM units" \n+ help="Beagle uses linear interpolation to estimate genetic positions between map positions. If \n+ no genetic map is specified, Beagle assumes a constant recombination rate of 1 cM per Mb"/>\n+ <param argument="excludesamples" type="data" format="txt" optional="true" label="Samples to exclude" \n+ help="It specifies a file containing samples (one sample identifier per line) to be excluded \n+ from the analysis" />\n+ <param argument="excludemarkers" type="data" format="txt" optional="true" label="Markers to exclude" \n+ help="It specifies a file containing markers (one marker per line) to be excluded from the \n+ analysis. Each line of the file can be either an identifier from a VCF record\xe2\x80\x99s ID field \n+ or a genomic coordinate in the format: CHROM:POS" />\n+ </section>\n+ <param argument="chrom" type="text" optional="true" label="Specify a chromosome interval" \n+ help="Input format: [chrom]:[start]-[end]. The entire chromosome, the beginning, or the end may be \n+ specified by chrom=[chrom], chrom=[chrom]:-[end], and chrom=[chrom]:[start]-, respectively">\n+ <saniti'..b's>\n+ </output>\n+ <output name="log_file" ftype="txt">\n+ <assert_contents>\n+ <has_text text="Reference markers: 223"/>\n+ <has_size value="1801" delta="10"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test ref bref3 input -->\n+ <test expect_num_outputs="1">\n+ <param name="gt" value="target.vcf.gz"/>\n+ <param name="ne" value="1000000"/>\n+ <param name="window" value="40.0"/>\n+ <param name="overlap" value="2.0"/>\n+ <section name="optional_inputs">\n+ <param name="ref" value="ref.bref3"/>\n+ </section>\n+ <section name="imputation_parameters">\n+ <param name="impute" value="true"/>\n+ <param name="imp_states" value="1600"/>\n+ <param name="imp_segment" value="6.0"/>\n+ <param name="imp_step" value="0.1"/>\n+ <param name="cluster" value="0.005"/>\n+ <param name="ap" value="true"/>\n+ <param name="gp" value="true"/>\n+ </section>\n+ <output name="vcf_file" ftype="vcf">\n+ <assert_contents>\n+ <has_text text=\'ID=GT,Number=1,Type=String,Description="Genotype"\'/>\n+ <has_size value="18635"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+.. class:: infomark\n+\n+**Purpose**\n+\n+Beagle is a program for phasing and imputing missing genotypes. Sporadic missing\n+genotypes are imputed during phasing. If a reference panel of phased genotypes is specified\n+with the ref argument, ungenotyped markers that are present in the reference panel can also\n+be imputed.\n+\n+Beagle version 5.2 provides significantly faster genotype phasing than version 5.1.\n+Recent versions of Beagle do not infer genotypes from genotype likelihood input data, but\n+Beagle versions 4.0 and 4.1 have this capability.\n+\n+----\n+\n+.. class:: infomark\n+\n+**HapMap genetic maps**\n+\n+HapMap genetic maps in PLINK format for GRCh36, GRCh37, and GRCh38 are available \n+in `this link <http://bochet.gcc.biostat.washington.edu/beagle/genetic_maps/>`_\n+\n+----\n+\n+.. class:: infomark\n+\n+**Input files**\n+\n+Beagle uses `Variant Call Format <http://faculty.washington.edu/browning/beagle/intro-to-vcf.html>`_ \n+(VCF) 4.3 for input and output genotype data. Pseuodoautosomal and non-pseudoautosomal \n+X-chromosome genotypes must be in separate input files and analysed separately unless male \n+haploid genotypes are coded as homozygous diploid genotypes.\n+\n+In the VCF file, if any heterozygote genotype is unphased (with "/" allele separator) in a marker window, \n+it will consider all heterozygote genotypes to be unphased, regardless of the allele separator used ("|" or "/").\n+Beagle assumes that an the VCF file has a name ending in ".gz" is compressed with gzip or bgzip, \n+and that a reference VCF file that has a name ending in \xe2\x80\x9c.bref3\xe2\x80\x9d is compressed with bref version 3.\n+\n+----\n+\n+.. class:: infomark\n+\n+**Output files**\n+\n+There are two output files. The log file gives a summary of the analysis that includes the\n+Beagle version, the command line arguments, and compute time.\n+\n+The vcf.gz file is a bgzip-compressed VCF file that contains phased, non-missing\n+genotypes for all non-reference samples. The output vcf.gz file can be uncompressed with the\n+unix gunzip utility.\n+\n+If a reference panel is specified and ungenotyped markers are imputed, the VCF INFO\n+field will contain:\n+\n+ ::\n+\n+ - A "DR2" subfield with the estimated squared correlation between the estimated allele dose and the true allele dose.\n+ - An "AF" subfield with the estimated alternate allele frequencies in the target samples.\n+ - The "IMP" flag if the marker is imputed.\n+ \n+ ]]> </help>\n+ <expand macro="citations" />\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 553b27c30eb8 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jul 03 23:33:37 2021 +0000 |
| b |
| @@ -0,0 +1,23 @@ +<macros> + <token name="@TOOL_VERSION@">5.2_21Apr21.304</token> + <token name="@SUFFIX_VERSION@">0</token> + <xml name="edam_ontology"> + <edam_topics> + <edam_topic>topic_0196</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0487</edam_operation> + </edam_operations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">beagle</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1016/j.ajhg.2018.07.015</citation> + <citation type="doi">10.1086/521987</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r 553b27c30eb8 test-data/plink.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plink.map Sat Jul 03 23:33:37 2021 +0000 |
| b |
| b'@@ -0,0 +1,664 @@\n+22 . 1.457757 15287922\n+22 . 1.585395 16370978\n+22 . 1.585931 16372046\n+22 . 1.586426 16373044\n+22 . 1.586781 16373740\n+22 . 1.587307 16374612\n+22 . 1.587384 16374641\n+22 . 1.58785 16374814\n+22 . 1.587972 16374956\n+22 . 1.588043 16375126\n+22 . 1.588197 16375526\n+22 . 1.58891 16377591\n+22 . 1.588919 16377625\n+22 . 1.589008 16378022\n+22 . 1.589064 16378306\n+22 . 1.589651 16381583\n+22 . 1.589799 16382408\n+22 . 1.594725 16384600\n+22 . 1.609336 16389667\n+22 . 1.611332 16390714\n+22 . 1.627759 16397311\n+22 . 1.628313 16397695\n+22 . 1.628891 16398802\n+22 . 1.631776 16406248\n+22 . 1.632396 16407851\n+22 . 1.632523 16408174\n+22 . 1.633008 16409399\n+22 . 1.633076 16409570\n+22 . 1.633081 16409581\n+22 . 1.633282 16410090\n+22 . 1.634329 16412723\n+22 . 1.63459 16413364\n+22 . 1.634662 16413538\n+22 . 1.63546 16415438\n+22 . 1.635482 16415484\n+22 . 1.635779 16416036\n+22 . 1.636006 16416156\n+22 . 1.642217 16419408\n+22 . 1.64826 16421699\n+22 . 1.657616 16425168\n+22 . 1.673904 16430832\n+22 . 1.674651 16431086\n+22 . 1.678997 16434967\n+22 . 1.679635 16435258\n+22 . 1.689342 16438107\n+22 . 1.691845 16456391\n+22 . 1.692015 16457636\n+22 . 1.694025 16472237\n+22 . 1.694045 16472379\n+22 . 1.694651 16476562\n+22 . 1.696055 16485919\n+22 . 1.696741 16490010\n+22 . 1.69716 16492336\n+22 . 1.699079 16502716\n+22 . 1.700217 16508400\n+22 . 1.700441 16509530\n+22 . 1.700462 16509636\n+22 . 1.708295 16549820\n+22 . 1.708311 16549902\n+22 . 1.708376 16550182\n+22 . 1.708835 16551808\n+22 . 1.717857 16568935\n+22 . 1.717906 16569017\n+22 . 1.718057 16569198\n+22 . 1.722988 16573830\n+22 . 1.724566 16575132\n+22 . 1.726139 16576248\n+22 . 1.726848 16576707\n+22 . 1.736799 16582469\n+22 . 1.740721 16584189\n+22 . 1.745161 16585842\n+22 . 1.749871 16586614\n+22 . 1.757703 16587858\n+22 . 1.766196 16589219\n+22 . 1.771946 16590153\n+22 . 1.777327 16591593\n+22 . 1.778797 16592176\n+22 . 1.782778 16594463\n+22 . 1.791565 16599488\n+22 . 1.799138 16603719\n+22 . 1.799255 16603872\n+22 . 1.801023 16606766\n+22 . 1.801054 16606815\n+22 . 1.802287 16608749\n+22 . 1.80882 16609584\n+22 . 1.835979 16613057\n+22 . 1.836479 16613859\n+22 . 1.837685 16615817\n+22 . 1.837779 16615974\n+22 . 1.838103 16616526\n+22 . 1.838994 16618217\n+22 . 1.839535 16619607\n+22 . 1.839689 16620021\n+22 . 1.840053 16621097\n+22 . 1.84024 16621714\n+22 . 1.840366 16622188\n+22 . 1.840511 16622827\n+22 . 1.840922 16624776\n+22 . 1.841052 16625404\n+22 . 1.841252 16626376\n+22 . 1.841265 16626440\n+22 . 1.841469 16627729\n+22 . 1.841552 16628260\n+22 . 1.841882 16631390\n+22 . 1.841887 16631452\n+22 . 1.842076 16635343\n+22 . 1.842349 16640996\n+22 . 1.842426 16642588\n+22 . 1.842466 16643417\n+22 . 1.842761 16649519\n+22 . 1.842861 16651600\n+22 . 1.843063 16655768\n+22 . 1.843187 16658337\n+22 . 1.843225 16659133\n+22 . 1.843253 16659703\n+22 . 1.843661 16668143\n+22 . 1.843699 16668410\n+22 . 1.844613 16671721\n+22 . 1.845323 16674094\n+22 . 1.845332 16674102\n+22 . 1.845999 16674493\n+22 . 1.853712 16678780\n+22 . 1.856619 16680396\n+22 . 1.862966 16683482\n+22 . 1.863187 16683588\n+22 . 1.863812 16683883\n+22 . 1.888043 16688632\n+22 . 1.894807 16690487\n+22 . 1.903517 16693023\n+22 . 1.907722 16694398\n+22 . 1.913181 16696185\n+22 . 1.914556 16696580\n+22 . 1.915719 16696904\n+22 . 1.916121 16697016\n+22 . 1.916512 16697125\n+22 . 1.917224 16697323\n+22 . 1.917288 16697340\n+22 . 1.917684 16697442\n+22 . 1.918776 16697696\n+22 . 1.928572 16699620\n+22 . 1.947367 16702213\n+22 . 1.963484 16705838\n+22 . 1.965919 16706386\n+22 . 1.967255 16706687\n+22 . 1.967752 16706799\n+22 . 1.967836 16706829\n+22 . 1.968194 16707168\n+22 . 1.968956 16708242\n+22 . 1.969 16708304\n+22 . 1.969362 16708828\n+22 . 1.969634 16709221\n+22 . 1.970027 16709793\n+22 . 1.970096 16709829\n+22 . 1.970141 16709840\n+22 . 1.975905 16711253\n+22 . 1.989036 16714378\n+22 . 1.989333 16714789\n+22 . 1.989416 16714977\n+22 . 1.98964 16715410\n+22 . 1.990617 16718108\n+22 . 1.991195 16719707\n+22 . 1.991919 16721712\n+22 . 1.992027 16722213\n+22 . 1.992414 16725140\n+22 . 1.992476 16725606\n+22 . 1.992991 16729428\n+22 . 1.9'..b'2348\n+22 . 2.605532 16962373\n+22 . 2.605587 16962491\n+22 . 2.606455 16964612\n+22 . 2.606673 16965267\n+22 . 2.606895 16965935\n+22 . 2.606925 16966024\n+22 . 2.606949 16966101\n+22 . 2.607306 16967253\n+22 . 2.607387 16967514\n+22 . 2.607608 16968225\n+22 . 2.608059 16969625\n+22 . 2.608069 16969648\n+22 . 2.608353 16970295\n+22 . 2.608588 16970820\n+22 . 2.608654 16970964\n+22 . 2.608705 16971076\n+22 . 2.609143 16972035\n+22 . 2.609162 16972076\n+22 . 2.609624 16973066\n+22 . 2.609865 16973596\n+22 . 2.609963 16973805\n+22 . 2.610097 16974055\n+22 . 2.610423 16974501\n+22 . 2.611468 16975883\n+22 . 2.611576 16976386\n+22 . 2.612041 16981295\n+22 . 2.612134 16982299\n+22 . 2.612446 16983139\n+22 . 2.612847 16984218\n+22 . 2.612861 16984285\n+22 . 2.612955 16985359\n+22 . 2.612976 16985601\n+22 . 2.613001 16985893\n+22 . 2.613012 16986028\n+22 . 2.613026 16986183\n+22 . 2.613055 16986521\n+22 . 2.61306 16986584\n+22 . 2.613078 16986794\n+22 . 2.61309 16986933\n+22 . 2.613195 16988136\n+22 . 2.614739 16988420\n+22 . 2.614828 16988668\n+22 . 2.615268 16989889\n+22 . 2.615491 16990464\n+22 . 2.615498 16990479\n+22 . 2.615824 16991142\n+22 . 2.615843 16991181\n+22 . 2.615928 16991349\n+22 . 2.616431 16992339\n+22 . 2.616986 16993799\n+22 . 2.617023 16993922\n+22 . 2.617068 16994124\n+22 . 2.617107 16994301\n+22 . 2.617209 16994764\n+22 . 2.617267 16995031\n+22 . 2.617296 16995174\n+22 . 2.619673 17007305\n+22 . 2.619764 17007540\n+22 . 2.62065 17007779\n+22 . 2.620908 17007837\n+22 . 2.624658 17008410\n+22 . 2.632835 17008656\n+22 . 2.633881 17008687\n+22 . 2.644593 17009000\n+22 . 2.680294 17010042\n+22 . 2.684729 17010694\n+22 . 2.688499 17011313\n+22 . 2.690061 17011562\n+22 . 2.691882 17011643\n+22 . 2.709499 17012292\n+22 . 2.713527 17012403\n+22 . 2.719617 17012541\n+22 . 2.723609 17012630\n+22 . 2.732041 17012818\n+22 . 2.732507 17012830\n+22 . 2.735013 17012902\n+22 . 2.745738 17013211\n+22 . 2.76118 17013657\n+22 . 2.762135 17014255\n+22 . 2.769639 17019000\n+22 . 2.769746 17019146\n+22 . 2.76988 17019527\n+22 . 2.770372 17021090\n+22 . 2.770438 17021301\n+22 . 2.771029 17023157\n+22 . 2.771391 17024055\n+22 . 2.775766 17032813\n+22 . 2.776091 17033482\n+22 . 2.777496 17036408\n+22 . 2.778489 17038689\n+22 . 2.778779 17039960\n+22 . 2.77918 17041917\n+22 . 2.779227 17042300\n+22 . 2.77935 17043300\n+22 . 2.779383 17043313\n+22 . 2.780586 17043679\n+22 . 2.780595 17043838\n+22 . 2.78063 17044465\n+22 . 2.780639 17044635\n+22 . 2.780642 17044694\n+22 . 2.780644 17044720\n+22 . 2.780662 17045080\n+22 . 2.780667 17045165\n+22 . 2.780689 17045599\n+22 . 2.780691 17045642\n+22 . 2.780719 17046173\n+22 . 2.780741 17046605\n+22 . 2.780759 17046957\n+22 . 2.780845 17048610\n+22 . 2.780849 17048693\n+22 . 2.780862 17048924\n+22 . 2.780892 17049480\n+22 . 2.781356 17050842\n+22 . 2.781603 17051559\n+22 . 2.78161 17051664\n+22 . 2.78163 17051999\n+22 . 2.78164 17052166\n+22 . 2.781661 17052506\n+22 . 2.781743 17053836\n+22 . 2.781767 17054234\n+22 . 2.781773 17054330\n+22 . 2.781792 17054630\n+22 . 2.781823 17055126\n+22 . 2.78183 17055255\n+22 . 2.781833 17055291\n+22 . 2.781854 17055501\n+22 . 2.781859 17055580\n+22 . 2.781865 17055665\n+22 . 2.781928 17056640\n+22 . 2.781948 17056940\n+22 . 2.781988 17057549\n+22 . 2.782012 17057918\n+22 . 2.782024 17058090\n+22 . 2.782034 17058239\n+22 . 2.782055 17058549\n+22 . 2.782062 17058654\n+22 . 2.782067 17058735\n+22 . 2.782071 17058788\n+22 . 2.78221 17060783\n+22 . 2.782223 17060968\n+22 . 2.78228 17061760\n+22 . 2.782308 17062158\n+22 . 2.782339 17062592\n+22 . 2.782435 17063944\n+22 . 2.782506 17064969\n+22 . 2.782717 17068081\n+22 . 2.782755 17068636\n+22 . 2.782824 17069528\n+22 . 2.783462 17072308\n+22 . 2.783811 17073464\n+22 . 2.783854 17074025\n+22 . 2.784028 17076254\n+22 . 2.784057 17076418\n+22 . 2.784794 17080623\n+22 . 2.784908 17081023\n+22 . 2.785761 17084017\n+22 . 2.785792 17084123\n+22 . 2.785804 17084145\n+22 . 2.786552 17085042\n+22 . 2.786866 17085316\n+22 . 2.787233 17085614\n+22 . 2.788557 17086809\n+22 . 2.788707 17086917\n+22 . 2.798148 17090465\n+22 . 2.804049 17090714\n+22 . 2.835789 17092051\n+22 . 2.903548 17094910\n' |
| b |
| diff -r 000000000000 -r 553b27c30eb8 test-data/ref.bref3 |
| b |
| Binary file test-data/ref.bref3 has changed |
| b |
| diff -r 000000000000 -r 553b27c30eb8 test-data/ref.vcf.gz |
| b |
| Binary file test-data/ref.vcf.gz has changed |
| b |
| diff -r 000000000000 -r 553b27c30eb8 test-data/target.vcf.gz |
| b |
| Binary file test-data/target.vcf.gz has changed |
| b |
| diff -r 000000000000 -r 553b27c30eb8 test-data/test.vcf.gz |
| b |
| Binary file test-data/test.vcf.gz has changed |
| b |
| diff -r 000000000000 -r 553b27c30eb8 test-data/test_output.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output.log Sat Jul 03 23:33:37 2021 +0000 |
| [ |
| @@ -0,0 +1,74 @@ +beagle.21Apr21.304.jar (version 5.2) +Copyright (C) 2014-2021 Brian L. Browning +Enter "java -jar beagle.21Apr21.304.jar" to list command line argument +Start time: 08:46 PM GMT on 26 Jun 2021 + +Command line: java -Xmx989m -jar beagle.21Apr21.304.jar + gt=/tmp/tmpoahokk9w/files/e/9/3/dataset_e93c5cb3-373e-4432-80ab-47ff1068bc9f.dat + chrom=22:100- + ne=1000000 + window=40.0 + overlap=2.0 + seed=1 + err=0.02 + burnin=3 + iterations=12 + phase-states=280 + impute=true + imp-states=1600 + imp-segment=6.0 + imp-step=0.1 + cluster=0.005 + ap=false + gp=false + out=out + nthreads=1 + +No genetic map is specified: using 1 cM = 1 Mb + +Reference samples: 0 +Study samples: 191 + +Window 1 [22:20000086-20016908] +Reference markers: 223 +Study markers: 223 + +Burnin iteration 1: 1 second + +Burnin iteration 2: 0 seconds + +Burnin iteration 3: 0 seconds + +Phasing iteration 1: 0 seconds + +Phasing iteration 2: 0 seconds + +Phasing iteration 3: 0 seconds + +Phasing iteration 4: 0 seconds + +Phasing iteration 5: 0 seconds + +Phasing iteration 6: 0 seconds + +Phasing iteration 7: 0 seconds + +Phasing iteration 8: 0 seconds + +Phasing iteration 9: 0 seconds + +Phasing iteration 10: 0 seconds + +Phasing iteration 11: 0 seconds + +Phasing iteration 12: 0 seconds + +Cumulative Statistics: + +Study markers: 223 + +Haplotype phasing time: 2 seconds +Total time: 3 seconds + +End time: 08:46 PM GMT on 26 Jun 2021 +beagle.21Apr21.304.jar finished |
| b |
| diff -r 000000000000 -r 553b27c30eb8 test-data/test_output.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_output.vcf Sat Jul 03 23:33:37 2021 +0000 |
| [ |
| b'@@ -0,0 +1,232 @@\n+##fileformat=VCFv4.2\n+##filedate=20210626\n+##source="beagle.21Apr21.304.jar"\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies">\n+##INFO=<ID=DR2,Number=A,Type=Float,Description="Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose">\n+##INFO=<ID=IMP,Number=0,Type=Flag,Description="Imputed marker">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=DS,Number=A,Type=Float,Description="estimated ALT dose [P(RA) + 2*P(AA)]">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00096\tHG00097\tHG00099\tHG00100\tHG00101\tHG00102\tHG00103\tHG00104\tHG00106\tHG00108\tHG00109\tHG00110\tHG00111\tHG00112\tHG00113\tHG00114\tHG00116\tHG00117\tHG00118\tHG00119\tHG00120\tHG00121\tHG00122\tHG00123\tHG00124\tHG00125\tHG00126\tHG00127\tHG00128\tHG00129\tHG00130\tHG00131\tHG00133\tHG00134\tHG00135\tHG00136\tHG00137\tHG00138\tHG00139\tHG00140\tHG00141\tHG00142\tHG00143\tHG00146\tHG00148\tHG00149\tHG00150\tHG00151\tHG00152\tHG00154\tHG00155\tHG00156\tHG00158\tHG00159\tHG00160\tHG00171\tHG00173\tHG00174\tHG00176\tHG00177\tHG00178\tHG00179\tHG00180\tHG00182\tHG00183\tHG00185\tHG00186\tHG00187\tHG00188\tHG00189\tHG00190\tHG00231\tHG00232\tHG00233\tHG00234\tHG00235\tHG00236\tHG00237\tHG00238\tHG00239\tHG00240\tHG00242\tHG00243\tHG00244\tHG00245\tHG00246\tHG00247\tHG00249\tHG00250\tHG00251\tHG00252\tHG00253\tHG00254\tHG00255\tHG00256\tHG00257\tHG00258\tHG00259\tHG00260\tHG00261\tHG00262\tHG00263\tHG00264\tHG00265\tHG00266\tHG00267\tHG00268\tHG00269\tHG00270\tHG00271\tHG00272\tHG00273\tHG00274\tHG00275\tHG00276\tHG00277\tHG00278\tHG00280\tHG00281\tHG00282\tHG00284\tHG00285\tHG00306\tHG00309\tHG00310\tHG00311\tHG00312\tHG00313\tHG00315\tHG00318\tHG00319\tHG00320\tHG00321\tHG00323\tHG00324\tHG00325\tHG00326\tHG00327\tHG00328\tHG00329\tHG00330\tHG00331\tHG00332\tHG00334\tHG00335\tHG00336\tHG00337\tHG00338\tHG00339\tHG00341\tHG00342\tHG00343\tHG00344\tHG00345\tHG00346\tHG00349\tHG00350\tHG00351\tHG00353\tHG00355\tHG00356\tHG00357\tHG00358\tHG00359\tHG00360\tHG00361\tHG00362\tHG00364\tHG00366\tHG00367\tHG00369\tHG00372\tHG00373\tHG00375\tHG00376\tHG00377\tHG00378\tHG00381\tHG00382\tHG00383\tHG00384\tHG00403\tHG00404\tHG00406\tHG00407\tHG00418\tHG00419\tHG00421\tHG00422\tHG00427\tHG00428\n+22\t20000086\trs138720731\tT\tC\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\n+22\t20000146\trs73387790\tG\tA\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\n+22\t20000199\trs183293480\tA\tC\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0'..b'\tA\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\n+22\t20016672\trs189265547\tC\tT\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\n+22\t20016702\trs142417111\tG\tA\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\n+22\t20016819\trs181826197\tC\tT\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\n+22\t20016908\trs186551893\tC\tT\t.\tPASS\t.\tGT\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\t0|0\n' |