Torrent Browser Analysis Report Guide
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Example Torrent Variant Caller Parameter File
This page contains an example JSON-format parameters file.
A file of this type is used to upload custom parameter settings to the Torrent Variant Caller (TVC) plugin (see Upload a JSON file of parameter values ). You can download a similar file with the settings used in your TVC run, with the plugin report Settings File button (see Variant Caller Report ).
{
"torrent_variant_caller": {
"snp_min_allele_freq": "0.15",
"snp_strand_bias": "0.95",
"hotspot_min_coverage": "20",
"hotspot_min_cov_each_strand": "3",
"hotspot_min_allele_freq": "0.15",
"snp_min_variant_score": "10",
"snp_beta_bias": "8",
"hotspot_strand_bias": "0.95",
"hp_max_length": "8",
"filter_insertion_predictions": "0.2",
"indel_min_variant_score": "10",
"indel_beta_bias": "8",
"indel_min_coverage": "20",
"heavy_tailed": "3",
"outlier_probability": "0.01",
"data_quality_stringency": "8.5",
"snp_min_cov_each_strand": "3",
"hotspot_min_variant_score": "10",
"indel_strand_bias": "0.85",
"downsample_to_coverage": "400",
"filter_unusual_predictions": "0.25",
"indel_min_allele_freq": "0.15",
"prediction_precision": "1",
"indel_min_cov_each_strand": "3",
"filter_deletion_predictions": "0.2",
"snp_min_coverage": "20",
"hotspot_beta_bias": "8"
},
"meta": {
"tvcargs": "tvc"
},
"long_indel_assembler": {
"short_suffix_match": "5",
"min_indel_size": "4",
"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": "0",
"read_max_mismatch_fraction": "1",
"allow_snps": "1",
"allow_indels": "1",
"min_mapping_qv": "4",
"gen_min_alt_allele_freq": "0.15",
"read_mismatch_limit": "10",
"min_base_qv": "4",
"gen_min_indel_alt_allele_freq": "0.15"
}
}
Torrent Browser Analysis Report Guide
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Plugin Summary
Assembler SPAdes Plugin
Coverage Analysis Plugin
ERCC Analysis Plugin
FileExporter Plugin
FilterDuplicates Plugin
IonReporterUploader Plugin
See
The Ion Reporter™ Software Integration Guide
Run RecognitION Plugin
SampleID Plugin
TorrentSuiteCloud Plugin
Torrent Variant Caller Plugin
Torrent Variant Caller Parameters
Example Torrent Variant Caller Parameter File
Torrent Variant Caller Output
The Command-Line Torrent Variant Caller
Ion Reporter™ Software Features Related to Variant Calling
Integration with TaqMan® and PCR