Ionchefplantemplate Resource ========================================================================== Resource URL: ``http://mytorrentserver/rundb/api/v1/ionchefplantemplate/`` Schema URL: ``http://mytorrentserver/rundb/api/v1/ionchefplantemplate/schema/`` .. include:: ../manual_api_ref_docs/ionchefplantemplate.rst Fields table ------------ ================================= ================================================================================================== ======= ======== ======== ===== ====== ======== field help text default nullable readonly blank unique type ================================= ================================================================================================== ======= ======== ======== ===== ====== ======== **planDisplayedName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoAnalyze** Boolean data. Ex: True n/a false false false false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **preAnalysis** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefStatus** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **applicationGroup** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **libkit** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **platform** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **categories** Unicode string data. Ex: "Hello World" true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planPGM** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planTotal** Integer data. Ex: 2673 0 false false false false integer --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **projects** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **notes** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sequencekitname** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **base_recalibration_mode** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **storageHost** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **expName** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **cycles** Integer data. Ex: 2673 n/a true false false false integer --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isReverseRun** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **storage_options** Unicode string data. Ex: "Hello World" A false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipType** Unicode string data. Ex: "Hello World" false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefProgress** Floating point numeric data. Ex: 26.73 0 false false true false float --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **library** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverselibrarykey** Unicode string data. Ex: "Hello World" false true false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleTubeLabel** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **seqKitBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **barcodeId** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefLogPath** Unicode string data. Ex: "Hello World" n/a true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isPlanGroup** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **realign** Boolean data. Ex: True n/a false false false false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleGroupingName** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **experiment** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **bedfile** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isReusable** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isDuplicateReads** Boolean data. Ex: True n/a false false false false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **librarykitname** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **adapter** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **tfKey** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **parentPlan** Unicode string data. Ex: "Hello World" None false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **forward3primeadapter** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **samplePrepKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **applicationGroupDisplayedName** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **metaData** Unicode string data. Ex: "Hello World" {} false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_uid** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isFavorite** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet_planIndex** Integer data. Ex: 2673 0 false false false false integer --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **qcValues** Many related resources. Can be either a list of URIs or list of individually nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planStatus** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingKitName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runType** Unicode string data. Ex: "Hello World" GENS false false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **username** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleDisplayedName** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **controlSequencekitname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefMessage** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **templatingSize** Unicode string data. Ex: "Hello World" true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **childPlans** A list of data. Ex: ['abc', 26.73, 8] [] false false false false list --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **pairedEndLibraryAdapterName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runMode** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **irworkflow** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecuted** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **project** Unicode string data. Ex: "Hello World" n/a false true true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePostBeadfind** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **libraryReadLength** Integer data. Ex: 2673 0 false false false false integer --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **runname** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planGUID** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planShortID** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSetGroupType** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sample** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **planExecutedDate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse_primer** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **id** Integer data. Ex: 2673 false false true true integer --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **barcodedSamples** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **regionfile** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **selectedPlugins** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSet** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isSystemDefault** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **autoName** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **libraryKey** Unicode string data. Ex: "Hello World" false false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **flows** Integer data. Ex: 2673 0 false false false false integer --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **date** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **isSystem** Boolean data. Ex: True false false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **variantfrequency** Unicode string data. Ex: "Hello World" false true false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleSetDisplayedName** Unicode string data. Ex: "Hello World" n/a true true true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **flowsInOrder** Unicode string data. Ex: "Hello World" true false true false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **sampleGrouping** A single related resource. Can be either a URI or set of nested resource data. n/a true false true false related --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chipBarcode** Unicode string data. Ex: "Hello World" n/a true false false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **usePreBeadfind** Boolean data. Ex: True false false true false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **resource_uri** Unicode string data. Ex: "Hello World" n/a false true false false string --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **reverse3primeadapter** Unicode string data. Ex: "Hello World" false true false false string ================================= ================================================================================================== ======= ======== ======== ===== ====== ======== Example request --------------- Request URL: ``http://mytorrentserver/rundb/api/v1/ionchefplantemplate/?format=json&limit=1`` Python example ^^^^^^^^^^^^^^ .. code-block:: python import requests ts_api_request = requests.get("http://mytorrentserver/rundb/api/v1/ionchefplantemplate/", params={"format": "json", "limit": 1}) ts_api_response = ts_api_request.json() ionchefplantemplates = ts_api_response["objects"] for ionchefplantemplate in ionchefplantemplates: print ionchefplantemplate Torrent Server response ^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: javascript { "meta": { "previous": null, "total_count": 17, "offset": 0, "limit": 1, "next": "/rundb/api/v1/ionchefplantemplate/?offset=1&limit=1&format=json" }, "objects": [ { "planDisplayedName": "IC_P1v2_VAL_ccp", "autoAnalyze": true, "templatingKitBarcode": null, "preAnalysis": true, "chefStatus": "", "applicationGroup": "/rundb/api/v1/applicationgroup/1/", "libkit": null, "platform": "", "categories": "", "planPGM": null, "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --max-phasing-levels 2", "alignmentargs": "stage1 map4", "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "sampleSet_planTotal": 0, "projects": [ "IC_P1v2_val" ], "notes": "", "sequencekitname": "IonProtonIHiQ", "base_recalibration_mode": "no_recal", "storageHost": null, "expName": "", "cycles": null, "isReverseRun": false, "storage_options": "A", "thumbnailalignmentargs": "stage1 map4", "chipType": "P1.1.17", "chefProgress": 0, "library": "hg19", "reverselibrarykey": "", "sampleTubeLabel": "", "seqKitBarcode": null, "barcodeId": "IonXpress", "chefLogPath": null, "isPlanGroup": false, "realign": false, "sampleGroupingName": "", "experiment": "/rundb/api/v1/experiment/32917/", "bedfile": "/results/uploads/BED/44/hg19/unmerged/detail/CCP.20131001.designed.bed", "isReusable": true, "isDuplicateReads": false, "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=100,100 --beadfind-thumbnail 1", "librarykitname": "Ion AmpliSeq 2.0 Library Kit", "adapter": null, "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1", "tfKey": "ATCG", "parentPlan": null, "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC", "planStatus": "pending", "samplePrepKitName": "", "applicationGroupDisplayedName": "DNA", "metaData": {}, "sampleSet_uid": null, "isFavorite": true, "sampleSet_planIndex": 0, "qcValues": [ { "threshold": 30, "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/", "id": 289314, "qcType": { "description": "", "minThreshold": 0, "maxThreshold": 100, "defaultThreshold": 30, "qcName": "Usable Sequence (%)", "id": 3, "resource_uri": "/rundb/api/v1/qctype/3/" }, "resource_uri": "/rundb/api/v1/plannedexperimentqc/289314/" }, { "threshold": 30, "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/", "id": 289313, "qcType": { "description": "", "minThreshold": 1, "maxThreshold": 100, "defaultThreshold": 30, "qcName": "Key Signal (1-100)", "id": 2, "resource_uri": "/rundb/api/v1/qctype/2/" }, "resource_uri": "/rundb/api/v1/plannedexperimentqc/289313/" }, { "threshold": 30, "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/", "id": 289312, "qcType": { "description": "", "minThreshold": 0, "maxThreshold": 100, "defaultThreshold": 30, "qcName": "Bead Loading (%)", "id": 1, "resource_uri": "/rundb/api/v1/qctype/1/" }, "resource_uri": "/rundb/api/v1/plannedexperimentqc/289312/" } ], "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=216,224 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", "thumbnailcalibrateargs": "calibrate --skipDroop", "templatingKitName": "Ion PROTON IC v2 Universal", "runType": "AMPS", "username": "ionuser", "planName": "IC_P1v2_VAL_ccp", "sampleDisplayedName": "", "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000", "controlSequencekitname": "", "chefMessage": "", "templatingSize": "200", "childPlans": [], "pairedEndLibraryAdapterName": "", "runMode": "single", "irworkflow": "", "planExecuted": false, "project": "IC_P1v2_val", "usePostBeadfind": false, "libraryReadLength": 200, "runname": null, "planGUID": "b55face2-df5f-434c-89df-210f384170cb", "planShortID": "IL9TF", "sampleSetGroupType": null, "sample": "", "planExecutedDate": null, "reverse_primer": null, "id": 111154, "barcodedSamples": {}, "regionfile": "/results/uploads/BED/47/hg19/unmerged/detail/CCP.20131001.hotspots.bed", "selectedPlugins": { "SystematicErrorAnalysis": { "userInput": "", "version": "0.8.5", "features": [], "name": "SystematicErrorAnalysis", "id": 734 }, "IonReporterUploader": { "userInput": { "accountName": "None", "userInputInfo": "", "accountId": "0" }, "version": "4.4.0.2", "features": [ "export" ], "name": "IonReporterUploader", "id": 993 }, "variantCaller": { "userInput": { "torrent_variant_caller": { "snp_min_allele_freq": "0.02", "snp_strand_bias": "0.95", "hotspot_min_coverage": 6, "hotspot_min_cov_each_strand": 2, "position_bias": "0.75", "hotspot_min_allele_freq": "0.01", "snp_min_variant_score": 6, "mnp_min_variant_score": 400, "hotspot_strand_bias": "0.95", "hp_max_length": 8, "filter_insertion_predictions": "0.2", "indel_min_variant_score": 6, "indel_min_coverage": 15, "heavy_tailed": 3, "outlier_probability": "0.005", "position_bias_ref_fraction": "0.05", "indel_strand_bias_pval": 1, "data_quality_stringency": "6.5", "snp_min_cov_each_strand": 0, "indel_as_hpindel": 0, "snp_strand_bias_pval": 1, "mnp_strand_bias": "0.95", "mnp_strand_bias_pval": 1, "hotspot_strand_bias_pval": 1, "hotspot_min_variant_score": 6, "do_mnp_realignment": 1, "indel_strand_bias": "0.9", "downsample_to_coverage": 2000, "filter_unusual_predictions": "0.3", "indel_min_allele_freq": "0.05", "mnp_min_allele_freq": "0.02", "mnp_min_coverage": 6, "do_snp_realignment": 1, "mnp_min_cov_each_strand": 0, "snp_min_coverage": 6, "prediction_precision": 1, "indel_min_cov_each_strand": 2, "filter_deletion_predictions": "0.2", "realignment_threshold": 1, "suppress_recalibration": 0, "position_bias_pval": "0.05", "use_position_bias": 0 }, "meta": { "ts_version": "4.4", "name": "Generic - Proton - Somatic - Low Stringency", "user_selections": { "chip": "proton_p1", "frequency": "somatic", "library": "ampliseq", "panel": "/rundb/api/v1/contentupload/48/" }, "librarytype": "ampliseq", "trimreads": true, "tooltip": "Parameter settings optimized for low frequency variants and minimum false negatives on Proton chips", "tvcargs": "tvc", "barcode_mode": "match", "based_on": "ampliseqexome_somatic_lowstringency_p1_parameters.json", "built_in": true, "configuration": "somatic_low_stringency_proton", "compatibility": { "chip": [ "proton_p1" ], "frequency": [ "somatic" ], "stringency": [ "low" ], "library": [ "wholegenome", "ampliseq", "targetseq" ] } }, "long_indel_assembler": { "min_indel_size": 4, "short_suffix_match": 5, "output_mnv": 0, "min_var_count": 5, "min_var_freq": "0.15", "kmer_len": 19, "max_hp_length": 8, "relative_strand_bias": "0.8" }, "freebayes": { "gen_min_coverage": 6, "allow_mnps": 1, "allow_complex": 0, "read_snp_limit": 10, "read_max_mismatch_fraction": 1, "allow_indels": 1, "min_mapping_qv": 4, "gen_min_alt_allele_freq": "0.035", "allow_snps": 1, "gen_min_indel_alt_allele_freq": "0.1" } }, "version": "4.4.0.6", "features": [], "name": "variantCaller", "id": 994 }, "validateVariantCaller": { "userInput": "", "version": "0.2.1", "features": [], "name": "validateVariantCaller", "id": 732 }, "validateVariantCaller-Lite": { "userInput": "", "version": "1.1.6", "features": [], "name": "validateVariantCaller-Lite", "id": 964 }, "coverageAnalysis": { "userInput": "", "version": "4.4.0.12", "features": [], "name": "coverageAnalysis", "id": 995 } }, "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600", "sampleSet": null, "isSystemDefault": false, "autoName": null, "libraryKey": "TCAG", "flows": 400, "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=100,100 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 1 --beadfind-thumbnail 1 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json", "date": "2015-01-28T19:57:42.000445+00:00", "isSystem": false, "variantfrequency": "", "sampleSetDisplayedName": "", "calibrateargs": "calibrate --skipDroop", "flowsInOrder": "", "sampleGrouping": null, "chipBarcode": null, "usePreBeadfind": true, "resource_uri": "/rundb/api/v1/ionchefplantemplate/111154/", "reverse3primeadapter": "" } ] } Allowed HTTP methods -------------------- - get - post - put - delete - patch