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nmdp-bioinformatics
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pipeline
Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
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Filter consensus sequences by expected ploidy
#81
ckennedy-nmdp
closed
9 years ago
1
Output consensus sequences and interpreted results in HML 1.0
#80
ckennedy-nmdp
closed
9 years ago
1
Adding script to generate reads from IMGT/HLA *_gen.fasta files
#79
ghost
closed
9 years ago
1
splitter should handle .fastq and .fq file extensions
#78
ckennedy-nmdp
closed
9 years ago
4
fix issue 76 with the power of regex
#77
janders3-nmdp
closed
9 years ago
0
pipeline should have better fastq detection
#76
janders3-nmdp
closed
9 years ago
1
misnamed variables.
#75
janders3-nmdp
closed
9 years ago
1
redhat lacks pidof. safer/easier to just not delete boilerplate header
#74
janders3-nmdp
closed
9 years ago
1
Unpaired FASTQ formatted sequences passed into SSAKE
#73
ghost
closed
9 years ago
2
ssake in homebrew (& linuxbrew)
#72
warrenlr
closed
9 years ago
1
sorted read bam indexing step specifies incorrect file name in process_fastq.bash line 155
#71
gturenchalk
closed
9 years ago
3
BOILERPLATE_HEADER file in process_fastq.bash gets prematurely deleted by first job to finish
#70
gturenchalk
closed
9 years ago
1
No interpretation for (some) HLA-A*11, *02, and *24 alleles
#69
ckennedy-nmdp
closed
9 years ago
1
Add option to remove alignment gaps '~' in the filtered consensus sequen...
#68
ckennedy-nmdp
closed
9 years ago
4
splice-bam.groovy doesn't properly filter HLA-A:23:38N
#67
ckennedy-nmdp
closed
9 years ago
6
improved splitting algorithm for BSD-derived Unix operating systems
#66
janders3-nmdp
closed
9 years ago
0
Samplecount v processorcount disparity fix
#65
janders3-nmdp
closed
9 years ago
3
fixes to boilerplate creation, should resolve issue #63
#64
janders3-nmdp
closed
9 years ago
0
process_fastq.sh does not create boilerplate_header.bcl
#63
janders3-nmdp
closed
9 years ago
1
Rhel osx support for splitter.bash
#62
janders3-nmdp
closed
9 years ago
0
Use reference sequences from GRCh38 instead of all_chr.fa
#61
ghost
closed
9 years ago
10
Have to index all_chr.fa.gz
#60
ckennedy-nmdp
closed
9 years ago
4
Keep intermediate files compressed throughout the pipeline
#59
ghost
closed
9 years ago
1
Is the ngs-fastq-to-ssake step still appropriate?
#58
ghost
closed
9 years ago
7
Fix bug #56, which is caused by improper formatting of regions files for...
#57
ckennedy-nmdp
closed
9 years ago
1
ArrayIndexOutOfBoundsException when filtering all HLA(-A) exons
#56
ckennedy-nmdp
closed
9 years ago
3
Fix issue #41 -- reverse complement minus strand HLA genes so they can b...
#55
ckennedy-nmdp
closed
9 years ago
1
New feature branch
#54
ckennedy-nmdp
closed
9 years ago
1
splitter.bash uses the split command in a form that won't work on all systems
#53
gturenchalk
closed
9 years ago
11
External Code Dependencies Should be Documented
#52
gturenchalk
opened
9 years ago
1
Would be nice if tutorial integrated minimal test data
#51
gturenchalk
closed
9 years ago
3
splitter/process_fastq have incomplete checks for required reference files
#50
janders3-nmdp
closed
9 years ago
1
called tools react poorly if called with entire genome as reference,but having less than 4gb of ram available.
#49
janders3-nmdp
closed
9 years ago
1
documentation/warning updates
#48
janders3-nmdp
closed
9 years ago
1
Merge method in splice-bam.groovy arbitrarily assigns contigs
#47
ckennedy-nmdp
closed
9 years ago
2
Output consensus FASTQ with MIRING headers (in HML)
#46
ckennedy-nmdp
closed
9 years ago
2
Would be great to find novel alleles and show polymorphisms that include regions outside exons 2 and 3 in class I genes and exon 2 in class II genes in the output.
#45
ybolon-nmdp
closed
9 years ago
1
Suggest allowing user to specify reference region in place of default full genome reference.
#44
ybolon-nmdp
closed
9 years ago
5
Capture requirements for interpretation service
#43
ghost
closed
9 years ago
3
Need regions files for class II HLA genes.
#42
ckennedy-nmdp
closed
9 years ago
3
Interpretation of HLA-B and -C alleles isn't working.
#41
ckennedy-nmdp
closed
9 years ago
3
Redirect mpileup (reads) output to file
#40
ckennedy-nmdp
closed
9 years ago
1
groovy script library requirements
#39
janders3-nmdp
closed
9 years ago
11
now splitter will find fastq files in subdirs at preliminary check - fix #37
#38
janders3-nmdp
closed
9 years ago
1
splitter.bash checks for fastq files differently than it finds them.
#37
janders3-nmdp
closed
9 years ago
0
cannot handle underscores in directory name
#36
ybolon-nmdp
closed
9 years ago
3
Adding Travis CI badge to readme
#35
ghost
closed
9 years ago
0
Add Travis CI badge to readme
#34
ghost
closed
9 years ago
0
Adding Travis CI configuration with no-op build script
#33
ghost
closed
9 years ago
0
can upgrade to post-HTSlib version of samtools and bcftools, here on github
#32
ybolon-nmdp
closed
9 years ago
3
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