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shane-c-lawson
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breseq
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VCF Output for Insertions does not follow VCFTools standard
#76
GoogleCodeExporter
closed
8 years ago
1
GD2VCF incorrectly reports AMP
#75
GoogleCodeExporter
closed
8 years ago
3
APPLY specific copy of MOB
#74
GoogleCodeExporter
closed
8 years ago
1
gd2gvf incorrect Ref nuclotide and strand
#73
GoogleCodeExporter
closed
8 years ago
3
Wrong junction candidate
#72
GoogleCodeExporter
opened
8 years ago
0
Translation of mutations may not deal with spliced genes and programmed frameshifts
#71
GoogleCodeExporter
opened
8 years ago
0
/usr/local/share/breseq/coverage_distribution.r: No such file or directory
#70
GoogleCodeExporter
closed
8 years ago
5
3 low quality snps (false positives) rather than 1 quality deletion. change in call between versions
#69
GoogleCodeExporter
opened
8 years ago
0
6 reads to support junction rather than 1bp snp
#68
GoogleCodeExporter
opened
8 years ago
0
gdtools gd2circos broken with newer Circos versions
#67
GoogleCodeExporter
opened
8 years ago
0
libbreseq/common.h build failure with clang 4.2 (elaborated type refers to a typedef)
#66
GoogleCodeExporter
closed
8 years ago
2
Evidence read stacks difficult
#65
GoogleCodeExporter
closed
8 years ago
1
HTML anchors for each table in index.html
#64
GoogleCodeExporter
opened
8 years ago
0
Visual distinction between syn/non-syn mutations
#63
GoogleCodeExporter
opened
8 years ago
1
Core dumps in breseq::pileup_base - assert failing
#62
GoogleCodeExporter
closed
8 years ago
4
breseq has two -j options, somewhat confusing
#61
GoogleCodeExporter
closed
8 years ago
1
0.21+ fails to build on OS X 10.7 with clang 4.1
#60
GoogleCodeExporter
closed
8 years ago
4
distant junctions rather than 9bp deletion
#59
GoogleCodeExporter
closed
8 years ago
1
ambiguous results being predicted with certanty
#58
GoogleCodeExporter
opened
8 years ago
0
index.html does not agree with output.gd
#57
GoogleCodeExporter
closed
8 years ago
3
IS186 junction not predicted because of equally probable matches
#56
GoogleCodeExporter
opened
8 years ago
0
3 event mutation: IS insertion, nearby IS insertion, deletion between IS elements
#55
GoogleCodeExporter
opened
8 years ago
0
MC coverage predicted rather than IS insertion
#54
GoogleCodeExporter
closed
8 years ago
3
Genome Diff to VCF function.
#53
GoogleCodeExporter
closed
8 years ago
4
junction location does not agree with sequence
#52
GoogleCodeExporter
closed
8 years ago
6
Support gzipped fastq files
#51
GoogleCodeExporter
opened
8 years ago
0
Failure during junction identification
#50
GoogleCodeExporter
closed
8 years ago
1
Use BAM instead of SAM for internal pipeline steps
#49
GoogleCodeExporter
opened
8 years ago
0
Predicting indel polymorphisms in homopolymer runs
#48
GoogleCodeExporter
opened
8 years ago
0
Move TACC commands to gdtools?
#47
GoogleCodeExporter
closed
8 years ago
2
Create binaries
#46
GoogleCodeExporter
opened
8 years ago
5
Junction sides incorrectly marked as redundant
#45
GoogleCodeExporter
opened
8 years ago
0
ERROR_COUNT segfaults (reusing existing BAM file)
#44
GoogleCodeExporter
closed
8 years ago
3
Incorporate mapping scores into mutation calls
#43
GoogleCodeExporter
opened
8 years ago
3
new junction predicted rather than 4bp deletion
#42
GoogleCodeExporter
closed
8 years ago
4
Methods to filter mutation predictions
#41
GoogleCodeExporter
closed
8 years ago
3
SMALT instead of SSAHA2?
#40
GoogleCodeExporter
closed
8 years ago
8
Translation table for yeast
#39
GoogleCodeExporter
closed
8 years ago
2
Multiple non-reference base polymorphisms
#38
GoogleCodeExporter
opened
8 years ago
1
Genome Diff entry errors
#37
GoogleCodeExporter
closed
8 years ago
2
Properly handle escaped characters from command line
#36
GoogleCodeExporter
closed
8 years ago
1
Incorrect call of IS3 mediated deletion
#35
GoogleCodeExporter
closed
8 years ago
4
Strand of junctions
#34
GoogleCodeExporter
closed
8 years ago
2
Deep Copy for cReferenceSequences
#33
GoogleCodeExporter
closed
8 years ago
1
Double listing of gene names in large deletions
#32
GoogleCodeExporter
closed
8 years ago
1
Clean up junction alignment HTML output
#31
GoogleCodeExporter
closed
8 years ago
2
Code cleanup tasks
#30
GoogleCodeExporter
closed
8 years ago
2
Add coverage info to summary table
#29
GoogleCodeExporter
closed
8 years ago
1
trimming alignment start/end for low quality Illumina bases
#28
GoogleCodeExporter
closed
8 years ago
2
Reads aligning at ends of reference sequences don't pass guards
#27
GoogleCodeExporter
opened
8 years ago
0
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