opencb hpg-bigdata issues

opencb / hpg-bigdata

This repository implements converters and tools for working with NGS data in HPC or Hadoop cluster

Apache License 2.0

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issues

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Add configuration file

#133 imedina closed 6 years ago
0
Remove old CLI for Hadoop

#132 imedina closed 6 years ago
0
Parallel implementation for converting (VCF to Avro/Parquet) and annotating variants

#131 jtarraga closed 7 years ago
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Annotate variants when converting VCF to Avro/Parquet

#130 jtarraga closed 7 years ago
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Compute stats for variants

#129 jtarraga opened 7 years ago
0
Support for PLINK, a third-party analysis tool for variants

#128 jtarraga opened 7 years ago
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Include sample filters using pedigree info when querying variants

#127 jtarraga opened 7 years ago
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Implement variant association analysis (chi-square, linear/logistic regression) using Spark MLlib

#126 jtarraga opened 7 years ago
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Support for rvtests, a third-party analysis tool for rare variants.

#125 jtarraga opened 7 years ago
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Add the -t/--num-threads parameter to the variant convert command line

#124 jtarraga closed 7 years ago
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Multithreaded Avro-Parquet converter

#123 jtarraga closed 7 years ago
0
Multithreaded VCF-Avro converter

#122 jtarraga closed 7 years ago
1
Multithreaded VCF-Parquet converter

#121 jtarraga closed 7 years ago
1
Add the --gene parameter to the variant query command line

#120 jtarraga closed 7 years ago
0
Add some hpg-bidata command line tests

#119 jtarraga closed 7 years ago
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Add sampleFilter for VariantDatasets

#118 jtarraga closed 7 years ago
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Fix bug in VariantDataset when filtering by proteinVariantAnnotation

#117 jtarraga closed 7 years ago
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Add the --group-by parameter to the variant query command line

#116 jtarraga closed 7 years ago
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Add the --sample-genotype parameter to the variant query command line

#115 jtarraga closed 7 years ago
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Add the --rename-cohort parameter to the variant metadata command line

#114 jtarraga closed 7 years ago
0
Reuse and clean code for the variant query (command line and web service)

#113 jtarraga closed 7 years ago
0
Create web service to execute variant queries

#112 jtarraga opened 8 years ago
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Compress the output file (variant query command line)

#111 jtarraga opened 8 years ago
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Save the variant query results in Parquet format

#110 jtarraga closed 7 years ago
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Save the variant query results in JSON format

#109 jtarraga closed 7 years ago
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Use the standard output and JSON format (variant query command line)

#108 jtarraga opened 8 years ago
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Rename the parameter --show to --limit in the variant query command line

#107 jtarraga closed 7 years ago
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Accept a file containing sample names as expected value for the --create-cohort parameter

#106 jtarraga closed 7 years ago
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Add the --create-cohort parameter to the variant metadata command line

#105 jtarraga closed 7 years ago
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Output aligment stats in plain text format

#104 jtarraga opened 8 years ago
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Improve JSON for alignment stats

#103 jtarraga opened 8 years ago
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Add the --summary parameter to the variant metadata command line

#102 jtarraga closed 7 years ago
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Add the --rename-dataset parameter to the variant metadata command line

#101 jtarraga closed 7 years ago
0
Add load/save pedigree parameters to the variant metadata command line

#100 jtarraga closed 7 years ago
0
Adopt the new variant metadata schema

#99 jtarraga closed 7 years ago
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Add the --from parameter to the alignment convert command line

#98 jtarraga closed 7 years ago
0
Convert BAM to Parquet without going through Avro

#97 jtarraga closed 7 years ago
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Add the necessary metadata parameters to the variant convert command line

#96 jtarraga closed 7 years ago
0
Add the --from parameter to the variant convert command line

#95 jtarraga closed 7 years ago
0
Convert VCF to Parquet without going through Avro

#94 jtarraga closed 7 years ago
0
Add the --schema parameter to the alignment and variant view command lines

#93 jtarraga closed 7 years ago
0
Create the 'variant metadata' command line

#92 jtarraga opened 8 years ago
0
Add the parameters --exclude-sequences and --exclude-qualities to the alignment view command line

#91 jtarraga opened 8 years ago
0
Add the --sam parameter to the alignment view command line

#90 jtarraga closed 7 years ago
0
Add the --vcf parameter to the variant view command line

#89 jtarraga opened 8 years ago
0
Add the parameters --exclude-samples and --exclude-annotations to the variant view command line

#88 jtarraga closed 7 years ago
0
Create the 'alignment view' command line

#87 jtarraga closed 7 years ago
0
Create the 'variant view' command line

#86 jtarraga closed 7 years ago
0
Support the --region-file parameter in the alignment query command

#85 jtarraga closed 7 years ago
0
Remove duplicate code in Alignment/VariantCommandExecutor

#84 jtarraga closed 7 years ago
0