dnanexus-archive parliament2 issues

dnanexus-archive / parliament2

Runs a combination of tools to generate structural variant calls on whole-genome sequencing data

Apache License 2.0

102 stars 39 forks source link

issues

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Fritz Lab will be developing and maintaining Parliament2

#91 cschin closed 4 years ago
0
Adding support for CRAM

#90 husamia opened 4 years ago
1
Running Parliament2 on multiple WGS sammples

#89 nitha26 opened 4 years ago
0
[E::hts_open_format] Failed to open file input.bam error

#88 info-97 opened 4 years ago
0
svviz_output

#87 gdaviduu opened 4 years ago
1
How to change bin_size parameter of CNVnator?

#86 adily777 opened 4 years ago
0
cp: cannot stat '/home/dnanexus/in/None': No such file or directory

#85 YTLogos closed 4 years ago
2
Access to test dataset

#84 ManavalanG opened 4 years ago
0
Correcting command to get help

#83 wdecoster opened 5 years ago
0
Question regarding using large WGS datasets

#82 oalavijeh opened 5 years ago
0
Is it ok to use svtyper on CNVnator?

#81 gevro opened 5 years ago
1
CNVnator error log

#80 lee039 opened 5 years ago
0
Parliament2 never terminates if running CNVnator with svtyper

#79 tfenne opened 5 years ago
0
Various bug fixes

#78 gevro opened 5 years ago
3
Attempt to move input BAM file?

#77 tfenne opened 5 years ago
2
Update Readme.md - add read group requirement information in readme

#76 sclan opened 5 years ago
0
Documentation touchup

#75 yihchii opened 5 years ago
0
Parliament2 v0.1.8 VS v0.1.10 - performances

#74 MaestSi opened 5 years ago
4
Updating to monitor memory usage while running svviz, as this

#73 slzarate closed 5 years ago
1
SSVIZ problem, job is taking too long

#72 jputerova closed 5 years ago
1
Configurable execution path at same location as BAM input.

#71 vladimirkovacevic opened 5 years ago
0
somatic SV

#70 feihongloveworld closed 5 years ago
1
Can't parse sequence for chromosome

#69 feihongloveworld opened 5 years ago
8
Add GRIDSS support

#68 d-cameron opened 5 years ago
1
"chr" always added to chromosome names in combined_genotyped.vcf

#67 vladimirkovacevic opened 5 years ago
0
V0.1.10 update

#66 slzarate closed 5 years ago
0
SVTyper bug fix

#65 slzarate closed 5 years ago
1
Parliament2 job got stuck and exceeded the timeoutpolicy

#64 sclan closed 5 years ago
0
Does Parliament2 run Delly translocations?

#63 vladimirkovacevic closed 5 years ago
1
Parliament2 for 10xG data on non-human genome

#62 MaestSi closed 5 years ago
2
Problem with a 7Mb targeted capture panel Illumina sequencing. "No such file or directory" error, cannot generate results.

#61 nelsonchanhk closed 5 years ago
1
Enable configurable paths for inputs, intermediate files and outputs in Docker image

#60 vladimirkovacevic opened 5 years ago
1
Parliament2 can also run for illumina mate-pairs reads instead paired end ?

#59 unique379r closed 5 years ago
1
cannot execute the parliament2 at a remote server

#58 mm538 closed 5 years ago
2
multiple bam files

#57 yyx8671 closed 5 years ago
2
Only CNVNATOR and DELLY outputs

#56 CWYuan08 closed 5 years ago
7
Sequence resolved calls in Parliament2 vcf file

#55 MaestSi closed 5 years ago
1
Changing travis yml to remove push stage

#54 slzarate closed 5 years ago
2
Add benchmarking outputs for manuscript

#53 slzarate closed 5 years ago
2
Manuscript update

#52 slzarate closed 5 years ago
0
MANTA is often killed after 6 hours before it completes

#51 davidcotter opened 5 years ago
6
AVGLEN slightly different from END-POS value

#50 MaestSi opened 5 years ago
4
Testing pull request

#49 sameerd closed 5 years ago
1
Reference index file is not optional for Manta

#48 davidcotter opened 5 years ago
1
Bug fix with docker push

#47 slzarate closed 5 years ago
0
Changes to get parliament2 working with Singularity on HPC systems

#46 sameerd closed 5 years ago
16
Breakseq2 for hg38-based bam files

#45 MaestSi opened 5 years ago
1
Error: No results were generated.

#44 yueyuanliu opened 5 years ago
3
Error: ERROR: An invalid (nonexistent) input file has been specified.

#43 rahulk87 closed 5 years ago
6
Can this be built on a non docker environment.

#42 RoydenClark closed 5 years ago
2