molgenis VaSeBuilder issues

molgenis / VaSeBuilder

Validation Set Builder

GNU Lesser General Public License v3.0

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issues

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Multi-base, multi-allele variants sometimes have different positions in the filtering list vs. original VCF.

#64 TDMedina closed 4 years ago
2
Implement usage of -s/--seed parameter

#63 MatthieuBeukers closed 5 years ago
1
Add VaSeBuilder uuid to other context output files

#62 MatthieuBeukers closed 5 years ago
0
Reverse acceptor filtering logic to increase speed.

#61 TDMedina closed 5 years ago
2
Missing variant ID's from debug log.

#60 TDMedina closed 5 years ago
1
Check acceptor/donor context id before adding to variant context

#59 MatthieuBeukers opened 5 years ago
0
Create linkfile between variant contexts and fastq output files

#58 MatthieuBeukers closed 5 years ago
1
Add method to use a mapping table to change sample names

#57 MatthieuBeukers closed 4 years ago
1
Add sanity checks during the run

#56 MatthieuBeukers opened 5 years ago
0
Implement specific runmodes in their own separate methods

#55 MatthieuBeukers closed 5 years ago
0
Patches for latest update.

#54 TDMedina closed 5 years ago
0
Add donor fastq reads semi randomly over the acceptors

#53 MatthieuBeukers closed 5 years ago
1
Acceptor reads not filtered properly in AC mode.

#52 TDMedina closed 5 years ago
1
FastQ R1 files are being written twice in AC mode.

#51 TDMedina closed 5 years ago
1
Add command used to output log.

#50 TDMedina closed 5 years ago
1
Using gender-mismatched donor/acceptors makes validation difficult.

#49 TDMedina opened 5 years ago
0
Add first methods for adding existing donor fastq files

#48 MatthieuBeukers closed 5 years ago
0
Major addition of multiple modes.

#47 TDMedina closed 5 years ago
0
Small update to unittests, start with implementation of sequence names in vcf and bam

#46 MatthieuBeukers closed 5 years ago
0
Start vasebuilder from an existing variant context file.

#45 TDMedina closed 5 years ago
1
Modified method to return only unique reads.

#44 TDMedina closed 5 years ago
0
Duplicate fastq records.

#43 TDMedina closed 5 years ago
1
Implement check that variant contexts themselves do not overlap

#42 MatthieuBeukers closed 5 years ago
1
Small updates to unittests

#41 MatthieuBeukers closed 5 years ago
0
First fix for using CRAM files

#40 MatthieuBeukers closed 5 years ago
0
Use reference when opening alignment files

#39 MatthieuBeukers closed 5 years ago
1
CRAM cache files are output to user's home directory.

#38 TDMedina closed 5 years ago
1
Updates to unittests

#37 MatthieuBeukers closed 5 years ago
0
Small bugfix.

#36 TDMedina closed 5 years ago
0
Allow users to supply a configuration file

#35 MatthieuBeukers closed 5 years ago
2
First implementation of using list files for donor VCF and BAM files

#34 MatthieuBeukers closed 5 years ago
0
Replaced missing argparse line for donor_only.

#33 TDMedina closed 5 years ago
0
Use a listing file for BAM/CRAM donor files to use

#32 MatthieuBeukers closed 5 years ago
1
Use of 'chr' for chromosomes

#31 MatthieuBeukers closed 5 years ago
2
Fixed acceptor exclusions.

#30 TDMedina closed 5 years ago
0
Add support for CRAM files

#29 MatthieuBeukers closed 5 years ago
0
Small updates, add command line parameter to vase.py

#28 MatthieuBeukers closed 5 years ago
0
Missing records in position stats files.

#27 TDMedina closed 5 years ago
1
Large changes to VaSeBuilder to expand features.

#26 TDMedina closed 5 years ago
0
add check for acceptor reads > 0

#25 MatthieuBeukers closed 5 years ago
0
Added outlier checking for variant context determination.

#24 TDMedina closed 5 years ago
0
Update to vaseutils and issue fix

#23 MatthieuBeukers closed 5 years ago
0
Catch errors in establishing variant context when no reads are found in BAM file.

#22 TDMedina closed 5 years ago
2
Change debug delimiters to tabs.

#21 TDMedina closed 5 years ago
1
Added option to output donor fastq files only, without acceptor fastqs.

#20 TDMedina closed 5 years ago
0
Update to make VaSeBuilder faster, update to VaSeUtils

#19 MatthieuBeukers closed 5 years ago
0
Added option to prevent fastq output.

#18 TDMedina closed 5 years ago
0
New mate method in master

#17 MatthieuBeukers closed 5 years ago
0
Fixed bad dictionary key reference.

#16 TDMedina closed 5 years ago
0
Remove mate() and use fetches to obtain read mates

#15 MatthieuBeukers closed 5 years ago
0

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