BD2KGenomics adam-contest-eval issues

BD2KGenomics / adam-contest-eval

Run ADAM variant calling against the 1000genomes.org dataset

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Compare FreeBayes against GATK results

#19 hannes-ucsc opened 9 years ago
0
Compare GATK results against published GATK runs against NA12878

#18 hannes-ucsc opened 9 years ago
0
Install Spark on single node in Azure

#17 hannes-ucsc opened 9 years ago
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Understand relationship between MarkDuplicates and Sort in ADAM

#16 hannes-ucsc closed 9 years ago
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Optimize cluster size and instance type for C835.HCC1143_BL.4.bam

#15 hannes-ucsc opened 9 years ago
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Use cgcloud to run ADAM on a C835.HCC1143_BL.4.bam

#14 hannes-ucsc opened 9 years ago
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Download one sample out of the Simon's Foundation Genome Diversity project from CGHub to S3

#13 beaunorgeot opened 9 years ago
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Assign ADAM ticket to Audrey

#12 hannes-ucsc closed 9 years ago
1
Set up Ubuntu node for Audrey on PODK

#11 hannes-ucsc closed 9 years ago
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Run 1000G Data through ADAM preprocessing on EC2. Use Ego/Luigee.

#10 beaunorgeot opened 9 years ago
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Talk to Frank about assigning ADAM ticket to Audrey

#9 hannes-ucsc closed 9 years ago
0
Assess quality of NA12878 variant calls, (Depends on results from #7 / #3)

#8 benedictpaten opened 9 years ago
1
Run GATK on low-coverage 1000G samples

#7 benedictpaten opened 9 years ago
2
Aligns sets up input files between ADAM/Avocado and GATK pipelines

#6 hannes-ucsc closed 9 years ago
0
Setup next planning meeting

#5 hannes-ucsc closed 9 years ago
2
Run SamBamba + FreeBayes on an PODK node against the 234G version of NA12878

#4 hannes-ucsc closed 9 years ago
7
Run GATK on i2.8xlarge instance against the 234G version of NA12878

#3 hannes-ucsc closed 9 years ago
0
Run ADAM+Avocado on i2.8xlarge instance against 234G version of NA12878

#2 hannes-ucsc opened 9 years ago
1
Try to reproduce problem running sort against 288GB version of NA12878 on 32 x r3.2xlarge

#1 hannes-ucsc opened 9 years ago
0