cancerit cgpPindel issues

cancerit / cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

http://cancerit.github.io/cgpPindel/

GNU Affero General Public License v3.0

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issues

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PCAP-core base image updated

#112 ThomasSClarke closed 2 months ago
2
Differing number of variant read counts for v3.3.0 and v3.5.0 and above

#111 sb43 opened 7 months ago
2
Feature/revcomp

#110 ThomasSClarke opened 1 year ago
0
Try to identify pindel output fields containing info related to Read Depth (mutated allele) and Reference Depth?

#109 ipstone opened 2 years ago
0
Feature/ignore contigs file

#108 davidrajones closed 2 years ago
1
applied masking to pindel output

#107 ThomasSClarke closed 2 years ago
0
Check for complex indel events

#106 ThomasSClarke opened 2 years ago
1
Feature/range based normal panel

#105 keiranmraine closed 2 years ago
2
NP only validating first coord

#104 keiranmraine closed 2 years ago
1
3.6.1 hotfix changes

#103 ThomasSClarke closed 2 years ago
0
FF019 div0 catch

#102 ThomasSClarke closed 2 years ago
1
Error on BAS file generation with bam_stats

#101 imendes93 closed 2 years ago
6
generated files are corrupt error

#100 imendes93 closed 2 years ago
2
call checking against BWA more robust, lots of testing to do

#99 keiranmraine closed 2 years ago
0
Release/3.6.0

#98 ThomasSClarke closed 2 years ago
0
Feature/flagging

#97 keiranmraine closed 2 years ago
0
single sample processing for pindel cohort

#96 keiranmraine opened 3 years ago
0
Feature/complex ins gt del

#95 keiranmraine closed 3 years ago
0
Release/b0.0.0

#94 keiranmraine closed 3 years ago
0
Circleci project setup

#93 keiranmraine closed 3 years ago
0
No Pindel Input performance improvement after 3.3.0 upgrade

#92 jsmedmar closed 4 years ago
8
Feature/revise dockerfile

#91 rulixxx closed 4 years ago
0
Naive question, does increasing -c in pindel input will make it faster?

#90 jsmedmar closed 4 years ago
3
Apply fix provided Bt Kai Ye/Xiaofei Yang to recover missed complex e…

#89 keiranmraine closed 4 years ago
0
Pindelpindel step hangs on high coverage chromosomes

#88 mflevine closed 4 years ago
6
IO hardening

#87 keiranmraine closed 5 years ago
1
Test under internal large CI system

#86 keiranmraine closed 5 years ago
1
I/O hardening - add validation to main code flow of pindel_input_gen.pl

#85 keiranmraine closed 5 years ago
1
I/O hardening - capture bytes written to each file

#84 keiranmraine closed 5 years ago
0
I/O hardening - tests for Sanger::CGP::Pindel::InputGen::reads_to_disk

#83 keiranmraine closed 5 years ago
0
I/O hardening - fill in stub function

#82 keiranmraine closed 5 years ago
0
I/O hardening - test cases

#81 keiranmraine closed 5 years ago
0
I/O hardening - stub function

#80 keiranmraine closed 5 years ago
0
Checking for corrupt intermediates

#79 keiranmraine closed 5 years ago
1
speed up flagging with ItervalTree

#78 keiranmraine opened 5 years ago
0
Pindel panel of normals

#77 DominikGlodzik closed 5 years ago
2
pindel_merge_vcf_bam.pl - output threads

#76 keiranmraine opened 5 years ago
0
input generation: high depth region speedup

#75 keiranmraine closed 5 years ago
2
Script to remove samples from a normal panel.

#74 keiranmraine closed 5 years ago
0
Possible to generate more records than input pairs

#73 keiranmraine closed 5 years ago
1
WIP: Fix bug introduced by 3.0.5 hotfix affecting species names

#72 keiranmraine closed 5 years ago
1
germline.bed - sort, compress, index

#71 keiranmraine opened 5 years ago
0
WIP Feature/docker full

#70 keiranmraine closed 5 years ago
0
Feature/docker

#69 ghost closed 5 years ago
2
Feature/single read qc fail handling and new pindel

#68 keiranmraine closed 5 years ago
1
updated pindel.cpp

#67 hliang0807 closed 5 years ago
0
handles species name with spaces in it

#66 sb43 closed 5 years ago
1
Add precommit checks

#65 keiranmraine opened 6 years ago
0
using the docker container of cgpPINDEL

#64 tanasa closed 6 years ago
1
using the docker container of cgpPINDEL

#63 tanasa closed 6 years ago
1