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tgen
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pegasusPipe
MIT License
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BWA Align memory usage
#46
PedalheadPHX
closed
6 years ago
1
rnaAlign.sh: rnaStrand variable never gets initialized
#45
denriquez
opened
6 years ago
5
Slurmified
#44
ryanrichholt
closed
6 years ago
0
Add SRA id parser to BWA mem readgroup id generation
#43
ryanrichholt
opened
6 years ago
0
Slurmified
#42
ryanrichholt
closed
6 years ago
0
Samtools sort seems to run long after bwa is done
#41
ryanrichholt
opened
6 years ago
0
Freebayes passes even when it crashes
#40
ryanrichholt
opened
6 years ago
0
Non-human recipes should not run GATK VariantAnnotator with human comparison files
#39
ryanrichholt
opened
6 years ago
0
checkProjectComplete.sh
#38
denriquez
opened
6 years ago
3
dnaAlignParts bug fix
#37
denriquez
closed
6 years ago
0
dnaAlignParts.sh doesn't check for R2 Fastq Pass
#36
denriquez
opened
6 years ago
5
Added statements to reset env when script is re-run
#35
denriquez
closed
6 years ago
0
added rm InQueue right before exit statements
#34
tgenahmet
closed
7 years ago
0
rnaAlign.sh script has a bug
#33
tgenahmet
opened
7 years ago
3
pegasus_germVcfMerge.pbs does not clear out *InQueue
#32
tgenahmet
opened
7 years ago
0
KHCR2 files added
#31
tgenahmet
closed
7 years ago
0
maxed out cuff* pbs scripts
#30
tgenahmet
closed
7 years ago
1
added GATK parameter to resolve file locking probmel
#29
tgenahmet
closed
7 years ago
0
max out cuffDiff cuffQuant and cuffLink to 10 days
#28
tgenahmet
closed
7 years ago
1
create STARREF entries for below in constants
#27
tgenahmet
closed
7 years ago
0
vcf tools normalize creates 0 byte index file
#26
tgenahmet
opened
7 years ago
3
md5sum being performed on the head node
#25
awchrist
opened
7 years ago
0
config file validation should make TRIPLET4ALLELECOUNT line is correct.
#24
tgenahmet
closed
7 years ago
1
emails notifications checks if email was already sent
#23
tgenahmet
closed
7 years ago
0
wrong FQ extension emails
#22
tgenahmet
closed
7 years ago
0
vcfMerger max time and file lock
#21
tgenahmet
closed
7 years ago
0
vcfMerger walltime
#20
tgenahmet
closed
7 years ago
0
recalibration fails because of quality score
#19
tgenahmet
opened
7 years ago
1
ped file format
#18
tgenahmet
opened
7 years ago
0
vcfMerger parsing sample names
#17
tgenahmet
closed
7 years ago
2
Max wall time
#16
tgenahmet
closed
7 years ago
0
change tophat fusion max walltime from 4 days to more days
#15
tgenahmet
closed
7 years ago
0
added AHCCC kit bed file paths
#14
tgenahmet
closed
7 years ago
0
GATK file lock
#13
tgenahmet
closed
7 years ago
3
update vcfMerger and cna steps with bed files for AHCCC
#12
tgenahmet
closed
7 years ago
0
corrected fail and inqueue files created by vcfMergerAC
#11
tgenahmet
closed
7 years ago
0
vcfMerger and mergeVcfAlleleCount
#10
tgenahmet
closed
7 years ago
2
STARREF95 needs to be created, and pointed to in constants.txt
#9
tgenahmet
closed
7 years ago
2
added elif option to find V6C bed files.
#8
tgenahmet
closed
7 years ago
0
merge vcf allele count now checks for correct file
#7
tgenahmet
closed
7 years ago
1
splitNCigar needs Xmx argument
#6
tgenahmet
opened
7 years ago
10
mergeVCFAlleleCount is not checking correctly if the job is already submitted
#5
tgenahmet
closed
7 years ago
4
vcfMerger.sh needs updated BED file
#4
tgenahmet
closed
7 years ago
1
bamText file initialized at every run and a couple of print statements
#3
tgenahmet
closed
7 years ago
0
samtools mpileup with multiple bams
#2
tgenahmet
closed
7 years ago
1
Added TSS2U support to cna15 and vcfMerger
#1
denriquez
closed
7 years ago
0