andyrimmer Platypus issues

andyrimmer / Platypus

Platypus Variant Caller

GNU General Public License v3.0

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issues

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Version on site http://www.well.ox.ac.uk/platypus not up-to-date

#44 duartemolha closed 7 years ago
0
Error: something is screwy

#43 walaj closed 8 years ago
3
>1bp SNPs?

#42 ulah opened 9 years ago
2
Variant calling on 454 RNAseq data

#41 ulah closed 8 years ago
1
Fixes Platypus such that it can be interrupted with ctrl-c

#40 jrandall closed 9 years ago
2
Platypus option details

#39 snewhouse closed 8 years ago
3
highly inbred species

#38 agolicz closed 8 years ago
1
Inconsistency of genotype and allele number

#37 przemekl opened 9 years ago
0
Platypus.py shebang line

#36 anthonycor closed 9 years ago
1
Update splitMNPsAndComplex.py

#35 hangphan closed 9 years ago
0
Missing variants at the beginning of a region when using only assembler

#34 hangphan opened 9 years ago
0
The best parameters for platypus

#33 SiyangLiu closed 8 years ago
1
Started adding htslib support

#32 dancooke closed 10 years ago
0
How to get the GL for multi variants (multi-allelic)

#31 cxue closed 8 years ago
1
Crash when running with Tophat BAMs

#30 andyrimmer closed 8 years ago
4
Merge gVCFs (N+1 Calling)

#29 andyrimmer opened 10 years ago
1
Merge multi-process VCF output in memory

#28 andyrimmer opened 10 years ago
0
Fixing platypus to output to stdout even when using multi-core.

#27 godotgildor closed 10 years ago
3
Update runner.py

#26 hangphan closed 10 years ago
1
Update variantutils.py

#25 hangphan closed 10 years ago
0
Update variantcaller.pyx

#24 hangphan closed 10 years ago
0
Update cpopulation.pyx

#23 hangphan closed 10 years ago
0
Fixes for 0.7.9.1 release (=> 0.7.9.2)

#22 chapmanb closed 10 years ago
2
Make Platypus output bgzipped VCF by default

#21 andyrimmer opened 10 years ago
0
Python 3 support

#20 andyrimmer opened 10 years ago
5
CRAM support using htslib/Samtools

#19 andyrimmer closed 9 years ago
1
VCF Validation

#18 dancooke closed 10 years ago
0
isSomaticCandidate() not defined in somaticMutationDetector.py

#17 hovestadt closed 10 years ago
1
Update samtoolsWrapper.pyx

#16 hangphan closed 10 years ago
0
Update samtoolsWrapper.pyx

#15 hangphan closed 10 years ago
4
Convert argparse options too booleans

#14 bgruening opened 10 years ago
2
Validate input VCf

#13 andyrimmer closed 10 years ago
1
Reference call qualities not well calibrated, and not conservative enough

#12 andyrimmer closed 10 years ago
1
Refernce Call block size shoud be configurable

#11 andyrimmer closed 10 years ago
1
segmentation fault, exit code 137

#10 seandavi closed 10 years ago
1
the same allele in multi-allelic variants & multiple records with same position

#9 WeijianYe opened 10 years ago
1
Very High memory use and allocation in 0.7.4 (and 0.7.2)

#8 aeonsim opened 10 years ago
7
Platypus should down-sample by default

#7 andyrimmer opened 10 years ago
0
No genotype likelihood for multi-allelic loci

#6 SiyangLiu opened 10 years ago
8
Import Error on MacOSX 10.9

#5 andyrimmer closed 10 years ago
1
Mapping quality issue with STAR

#4 andyrimmer opened 10 years ago
1
Assembler suggests variants that fail minReads filter

#3 andyrimmer opened 10 years ago
0
Filtering in genotyping mode

#2 mathii opened 10 years ago
0
Argument parsing: silently ignores misformed arguments

#1 mathii opened 10 years ago
0