plagnollab DNASeq_pipeline issues

plagnollab / DNASeq_pipeline

Pipeline in place at the UGI for DNA level analysis

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issues

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UCLex release 2105b chr 20 issue

#35 pontikos opened 9 years ago
3
Problem with annotate.sh

#34 APLevine opened 9 years ago
1
Post VEP processing bug

#33 APLevine closed 9 years ago
1
Add extra switches from setup script

#32 davenomiddlenamecurtis opened 9 years ago
1
ExAC/ESP

#31 APLevine closed 9 years ago
1
more non-set output dir

#30 vplagnol closed 9 years ago
3
Creating scripts folder in align mode

#29 vplagnol closed 9 years ago
9
VEP plugin for loss of function transcript effect estimator

#28 pontikos opened 9 years ago
6
Python script to convert xls to csv

#27 pontikos closed 9 years ago
2
Split multiallelic VCF into single allelic VCF

#26 pontikos closed 9 years ago
1
liftOver build 37 to build 38

#25 pontikos opened 9 years ago
1
Sort out the eQTL pipeline files

#24 kittyl opened 9 years ago
0
Get Picard CalculateHsMetrics working on BAM files.

#23 pontikos opened 9 years ago
0
Quality controls

#22 pontikos opened 9 years ago
0
VEP annotation

#21 pontikos opened 9 years ago
10
mitochondrial DNA

#20 pontikos opened 9 years ago
3
naming issues

#19 vplagnol closed 9 years ago
2
copy license from novoalign

#18 vplagnol closed 9 years ago
2
reformatting of VEP output for R and Excel

#17 pontikos closed 9 years ago
22
supportFrame issue

#16 vplagnol closed 9 years ago
3
Condel.pm

#15 pontikos closed 9 years ago
1
CombineGVCFs: ERROR input alleles must contain <NON_REF>

#14 pontikos closed 9 years ago
9
Add a Gitter chat badge to README.md

#13 gitter-badger closed 9 years ago
0
Clarified logic of not creating new bam if bam.bai is OK

#12 davenomiddlenamecurtis closed 9 years ago
0
novoalign error: Failed to read block data

#11 pontikos opened 9 years ago
3
Error: Stale NFS file handle

#10 pontikos closed 9 years ago
1
Error samblaster: Missing header on input sam file. Exiting.

#9 pontikos closed 9 years ago
6
Scripts for adding read groups

#8 davenomiddlenamecurtis closed 9 years ago
4
chromosome name in reference fasta and -L option

#7 pontikos closed 9 years ago
2
Add CNV calls to the WGS pipeline

#6 vplagnol closed 9 years ago
0
Error and output files- add job number

#5 vplagnol closed 9 years ago
0
Split the repo based on smaller subunits

#4 vplagnol closed 9 years ago
0
Genome-wide gVCF files?

#3 vplagnol closed 9 years ago
3
Email notifications

#2 pontikos closed 9 years ago
2
Implement sanity checks

#1 pontikos opened 9 years ago
9