stefinfection RUFUS issues

stefinfection / RUFUS

RUFUS k-mer based genomic variant detection

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Fix no genotype lines in VCF that bricks post-processing

#24 stefinfection opened 2 months ago
1
Include indels greater than 50bp in SVTYPE label

#23 stefinfection opened 2 months ago
0
Add actual read count output and fraction per variant in vcf instead of just kmer counts

#22 stefinfection opened 4 months ago
0
Determine source of non-determinism in rufus output

#21 stefinfection opened 4 months ago
1
Gather what base numbers are for rufus vcf filters + add ability to let user specify filtering cutoffs (for SG VQS project)

#20 stefinfection opened 5 months ago
0
Make documentation regarding build more clear - e.g. the 1000G file needs a build in it or change command line option to just use a build instead of specifying ref/1000G file

#19 stefinfection opened 5 months ago
0
Add SG's inherited variants filter to main script to run post vcf generation

#18 stefinfection opened 5 months ago
1
Test container on slurm system for CHPC

#17 stefinfection opened 5 months ago
0
Change 1000G filter to gnomAD one

#16 stefinfection opened 5 months ago
1
Get rid of leftover pipes during RUFUS run

#15 stefinfection opened 5 months ago
0
Investigate why there is a sensitivity issue for 120X 90-95% AF variants (FD-all samples from seqc2 consortia)

#14 stefinfection opened 7 months ago
0
Investigate variants that RUFUS didn't call from gold-standard dataset - specifically those that had contigs made but no variant calls

#13 stefinfection opened 7 months ago
1
Transfer all of the bam files including genentech ones

#12 stefinfection opened 8 months ago
0
Spec out existing exome functionality

#11 stefinfection opened 8 months ago
0
Create docker container for existing version of rufus

#10 stefinfection opened 8 months ago
0
Review seqc2 benchmarking data set thoroughly

#9 stefinfection opened 8 months ago
1
Download all bam files, run coverage tool on each of the bam files

#8 stefinfection opened 8 months ago
0
Complete c++ tutorial

#7 stefinfection opened 9 months ago
1
Do time and space complexity analysis on each of the main functions

#6 stefinfection opened 9 months ago
0
Add dependencies to UML diagram

#5 stefinfection opened 9 months ago
0
Add rufus command line to header of vcf

#4 stefinfection opened 9 months ago
0
Select data set to run rufus warm-up on

#3 stefinfection opened 9 months ago
1
Make outline of complete test coverage to run at release intervals for proof of correctness

#2 stefinfection opened 9 months ago
1
Create optional argument for root directory for ease of use in running on CHPC

#1 stefinfection opened 10 months ago
0