opencb/hpg-bigdata
This repository implements converters and tools for working with NGS data in HPC or Hadoop cluster
JavaApache-2.0
Issues
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Add configuration file
#133 opened by imedina - 0
Remove old CLI for Hadoop
#132 opened by imedina - 0
Add some hpg-bidata command line tests
#119 opened by jtarraga - 1
Multithreaded VCF-Parquet converter
#121 opened by jtarraga - 1
Multithreaded VCF-Avro converter
#122 opened by jtarraga - 0
Parallel implementation for converting (VCF to Avro/Parquet) and annotating variants
#131 opened by jtarraga - 0
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Multithreaded Avro-Parquet converter
#123 opened by jtarraga - 0
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Accept a file containing sample names as expected value for the --create-cohort parameter
#106 opened by jtarraga - 0
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Add sampleFilter for VariantDatasets
#118 opened by jtarraga - 0
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Adopt the new variant metadata schema
#99 opened by jtarraga - 0
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Save the variant query results in JSON format
#109 opened by jtarraga - 0
Save the variant query results in Parquet format
#110 opened by jtarraga - 0
Create the 'variant view' command line
#86 opened by jtarraga - 0
Create the 'alignment view' command line
#87 opened by jtarraga - 0
Add the parameters --exclude-samples and --exclude-annotations to the variant view command line
#88 opened by jtarraga - 0
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Compute stats for variants
#129 opened by jtarraga - 0
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Implement variant association analysis (chi-square, linear/logistic regression) using Spark MLlib
#126 opened by jtarraga - 0
Create web service to execute variant queries
#112 opened by jtarraga - 0
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Output aligment stats in plain text format
#104 opened by jtarraga - 0
Improve JSON for alignment stats
#103 opened by jtarraga - 0
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Add the parameters --exclude-sequences and --exclude-qualities to the alignment view command line
#91 opened by jtarraga - 0
Create the 'variant metadata' command line
#92 opened by jtarraga