Availableionchefplannedexperiment Resource ========================================================================== Resource URL: ``http://mytorrentserver/rundb/api/v1/availableionchefplannedexperiment/`` Schema URL: ``http://mytorrentserver/rundb/api/v1/availableionchefplannedexperiment/schema/`` .. include:: ../manual_api_ref_docs/availableionchefplannedexperiment.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 --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **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 0.0 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 false 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 --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **chefLastUpdate** A date & time as a string. Ex: "2010-11-10T03:07:43" n/a true false false false datetime --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **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 --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **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 --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **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 --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **base_recalibrate** Boolean data. Ex: True n/a false false false false boolean --------------------------------- -------------------------------------------------------------------------------------------------- ------- -------- -------- ----- ------ -------- **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/availableionchefplannedexperiment/?format=json&limit=1`` Python example ^^^^^^^^^^^^^^ .. code-block:: python import requests ts_api_request = requests.get("http://mytorrentserver/rundb/api/v1/availableionchefplannedexperiment/", params={"format": "json", "limit": 1}) ts_api_response = ts_api_request.json() availableionchefplannedexperiments = ts_api_response["objects"] for availableionchefplannedexperiment in availableionchefplannedexperiments: print availableionchefplannedexperiment Torrent Server response ^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: javascript { "meta": { "previous": null, "total_count": 10, "offset": 0, "limit": 1, "next": "/rundb/api/v1/availableionchefplannedexperiment/?offset=1&limit=1&format=json" }, "objects": [ { "planDisplayedName": "C18S2_package1_Thur_psp4", "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 --calibration-training=100000 --flow-signals-type scaled-residual --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": [ "Chef_p1v2_dev_IE" ], "notes": "148420", "sequencekitname": "ProtonIIC200Kit", "storageHost": null, "expName": "", "cycles": null, "isReverseRun": false, "storage_options": "A", "thumbnailalignmentargs": "stage1 map4", "chipType": "P1.1.17", "chefProgress": 0.0, "library": "hg19", "reverselibrarykey": "", "sampleTubeLabel": "00049613", "seqKitBarcode": null, "barcodeId": "IonXpress", "chefLogPath": null, "isPlanGroup": false, "realign": false, "sampleGroupingName": "", "experiment": "/rundb/api/v1/experiment/23817/", "bedfile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", "isReusable": false, "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", "chefLastUpdate": null, "samplePrepKitName": "Ion AmpliSeq Exome Kit", "applicationGroupDisplayedName": "DNA", "metaData": {}, "sampleSet_uid": null, "isFavorite": false, "sampleSet_planIndex": 0, "qcValues": [ { "threshold": 30, "plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/", "id": 266238, "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/266238/" }, { "threshold": 30, "plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/", "id": 266237, "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/266237/" }, { "threshold": 30, "plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/", "id": 266236, "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/266236/" } ], "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 PI IC 200 Kit", "runType": "AMPS_EXOME", "username": "ionuser", "planName": "C18S2_package1_Thur_psp4", "sampleDisplayedName": "", "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000 --calibration-training=100000 --flow-signals-type scaled-residual", "controlSequencekitname": "", "chefMessage": "", "childPlans": [], "pairedEndLibraryAdapterName": "", "runMode": "single", "irworkflow": "", "planExecuted": false, "project": "Chef_p1v2_dev_IE", "usePostBeadfind": false, "runname": null, "planGUID": "994fd167-7d5a-43e5-acca-c8ffa069350e", "planShortID": "0KXAK", "sampleSetGroupType": null, "sample": "", "planExecutedDate": null, "reverse_primer": null, "id": 102054, "barcodedSamples": { "1": { "barcodeSampleInfo": { "IonXpress_001": { "description": "", "reference": "hg19", "targetRegionBedFile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed", "hotSpotRegionBedFile": "", "nucleotideType": "DNA", "controlSequenceType": "", "externalId": "" } }, "barcodes": [ "IonXpress_001" ] } }, "regionfile": "", "selectedPlugins": { "coverageAnalysis": { "userInput": "", "version": "4.2-r88700", "features": [], "name": "coverageAnalysis", "id": 827 }, "validateVariantCaller": { "userInput": { "variant_caller_name": "variantCaller", "truth_major_snp": "NA12878_NIST_NoChrY_SNP.bed", "region": "NIST", "sample": "NA12878", "truth_minor_snp": "None", "truth_major_indel": "NA12878_NIST_NoChrY_indel.bed", "truth_minor_indel": "None" }, "version": "0.2.1", "features": [], "name": "validateVariantCaller", "id": 732 }, "variantCaller": { "userInput": { "torrent_variant_caller": { "snp_min_allele_freq": "0.10000000000000001", "snp_strand_bias": "0.97999999999999998", "hotspot_min_coverage": 6, "hotspot_min_cov_each_strand": 3, "hotspot_min_allele_freq": "0.10000000000000001", "snp_min_variant_score": 15, "hotspot_strand_bias": "0.94999999999999996", "hp_max_length": 8, "filter_insertion_predictions": "0.20000000000000001", "indel_min_variant_score": 20, "indel_min_coverage": 10, "heavy_tailed": 3, "outlier_probability": "0.01", "data_quality_stringency": 5, "snp_min_cov_each_strand": 0, "hotspot_min_variant_score": 10, "indel_strand_bias": "0.90000000000000002", "tvc_parameters_version": "germline_low_stringency_proton-3.6.66827", "downsample_to_coverage": 400, "filter_unusual_predictions": "0.25", "indel_min_allele_freq": "0.14999999999999999", "do_snp_realignment": 1, "prediction_precision": 1, "indel_min_cov_each_strand": 5, "filter_deletion_predictions": "0.20000000000000001", "suppress_recalibration": 0, "snp_min_coverage": 5 }, "meta": { "repository_id": "", "ts_version": "4.0", "name": "External file AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json", "user_selections": { "chip": "proton_p1", "frequency": "germline", "library": "ampliseq", "panel": "/rundb/api/v1/contentupload/53/" }, "librarytype": "ampliseq", "trimreads": true, "tooltip": "Retrieved from external file", "tvcargs": "tvc", "built_in": false, "configuration": "", "compatibility": {} }, "long_indel_assembler": { "min_indel_size": 4, "short_suffix_match": 5, "output_mnv": 0, "min_var_count": 5, "min_var_freq": "0.14999999999999999", "kmer_len": 19, "max_hp_length": 8, "relative_strand_bias": "0.80000000000000004" }, "freebayes": { "gen_min_coverage": 5, "allow_mnps": 1, "allow_complex": 0, "read_max_mismatch_fraction": 1, "read_mismatch_limit": 10, "allow_indels": 1, "min_mapping_qv": 4, "gen_min_alt_allele_freq": "0.10000000000000001", "allow_snps": 1, "gen_min_indel_alt_allele_freq": "0.14999999999999999" } }, "version": "4.2-r88446", "features": [], "name": "variantCaller", "id": 826 }, "AmpliconStats": { "userInput": "", "version": "0.4.5", "features": [], "name": "AmpliconStats", "id": 774 } }, "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600", "sampleSet": null, "isSystemDefault": false, "autoName": null, "libraryKey": "TCAG", "flows": 520, "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": "2014-06-26T04:47:43.000023+00:00", "isSystem": false, "variantfrequency": "", "sampleSetDisplayedName": "", "calibrateargs": "calibrate --skipDroop", "flowsInOrder": "", "sampleGrouping": null, "base_recalibrate": true, "chipBarcode": null, "usePreBeadfind": true, "resource_uri": "/rundb/api/v1/availableionchefplannedexperiment/102054/", "reverse3primeadapter": "" } ] } Allowed HTTP methods -------------------- - get - post - put - delete - patch