hammerlab variant-calling-benchmarks issues

hammerlab / variant-calling-benchmarks

Automated and curated variant calling benchmarks for Guacamole

Apache License 2.0

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issues

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Generate data with Mitty?

#41 hammer opened 7 years ago
0
Seraseq™ Solid Tumor Mutation Mix

#40 hammer opened 7 years ago
0
A somatic reference standard for cancer genome sequencing

#39 arahuja opened 7 years ago
0
SKBR3 PacBio Sequencing

#38 hammer opened 7 years ago
1
Texas Cancer Research Biobank (TCRB) data

#37 hammer opened 7 years ago
0
Mutect calls for dream

#36 timodonnell closed 7 years ago
0
Add pt189

#35 timodonnell closed 7 years ago
0
Fixes

#34 timodonnell closed 7 years ago
0
Support for submitting results to google cloud bucket

#33 timodonnell closed 7 years ago
0
investigate using bcbio-nextgen docker image running on gcloud to generate comparison calls

#32 timodonnell opened 7 years ago
0
Better configuration system, configurable `spark-submit` and env vars

#31 timodonnell closed 7 years ago
2
Add instructions for syncing results to google cloud bucket

#30 timodonnell closed 7 years ago
0
bzip2 compress result VCF and CSVs

#29 timodonnell closed 7 years ago
0
Support running benchmarks on mutect + strelka

#28 timodonnell opened 7 years ago
5
num-executors in demeter.json

#27 arahuja closed 7 years ago
1
Add DREAM synth1 benchmark and variants from VCF

#26 arahuja closed 7 years ago
2
Remove duplicate argument

#25 timodonnell closed 7 years ago
0
consider better ways of specifying guacamole jars

#24 timodonnell opened 7 years ago
0
Fix local run to use guacamole dependencies jar

#23 timodonnell closed 7 years ago
1
local run example is wrong, uses outdated guacamole-with-dependencies jar

#22 timodonnell closed 7 years ago
1
setup a nightly run

#21 timodonnell opened 7 years ago
2
figure out how to test, setup travis and coveralls

#20 timodonnell opened 7 years ago
0
First cut on vcb-guacamole-cluster script

#19 timodonnell closed 7 years ago
1
specificity computation

#18 arahuja closed 7 years ago
1
Document benchmark.json

#17 arahuja opened 7 years ago
1
Add PT189 benchmark

#16 timodonnell opened 7 years ago
0
create results directory

#15 arahuja closed 7 years ago
1
Fix local-wgs1 benchmark

#14 timodonnell closed 7 years ago
0
no good calls in local-wgs1 benchmark

#13 timodonnell closed 7 years ago
2
support running on google cloud

#12 timodonnell closed 7 years ago
1
support running on demeter

#11 timodonnell closed 7 years ago
0
First cut

#10 timodonnell closed 7 years ago
0
PANCREATIC CANCER - AU

#9 arahuja opened 8 years ago
0
Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

#8 arahuja opened 8 years ago
0
Add DREAM synthetic data

#7 timodonnell opened 8 years ago
0
add updated Illumina platnium dataset of high quality germline calls

#6 timodonnell opened 8 years ago
0
Download AML31 data from "Optimizing Cancer Genome Sequencing and Analysis"

#5 timodonnell opened 8 years ago
15
Look into data for "A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing"

#4 timodonnell opened 8 years ago
0
Add TCGA samples with validated variants

#3 timodonnell opened 8 years ago
0
Add checkpoint trials data where there is IMPACT or other panel

#2 timodonnell opened 8 years ago
0
Add AOCS patient 034 to establish data schema and workflow

#1 timodonnell closed 7 years ago
1