Clinical-Genomics-Lund SomaticPanelPipeline issues

Clinical-Genomics-Lund / SomaticPanelPipeline

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Tnscope problem with the insertion AF and AD calcuation

#67 sailepradh opened 1 month ago
0
Features/idsnp qc

#66 sailepradh opened 2 months ago
1
Incorrect Handling of Contamination Values

#65 ramsainanduri closed 2 months ago
1
Processes Fail to Execute When 'purity' Field Is Empty in CSV Input

#64 ramsainanduri opened 2 months ago
0
Fix cnv for Myeloid profile

#63 ramsainanduri opened 2 months ago
0
Finalizing Myeloid profile

#62 ramsainanduri opened 2 months ago
0
coyote cli preparations

#61 ViktorHy closed 2 months ago
4
corrected faulty header, needed for pysam

#60 ViktorHy closed 2 months ago
0
Add support for Pindel

#59 ramsainanduri opened 3 months ago
0
Add readthedocs

#58 ramsainanduri opened 3 months ago
0
Increase Sampling Limit from 50M to 75M for Solid & PARP workflow

#57 ramsainanduri closed 3 months ago
1
ID_SNPs based sample identification

#56 sailepradh opened 3 months ago
0
Changed pgx csv dir

#55 ramsainanduri closed 4 months ago
0
Cdm qc bug fix

#54 ramsainanduri closed 4 months ago
0
Fixed bam names in pgx csv

#53 ramsainanduri closed 4 months ago
0
CMD QC import

#52 ramsainanduri closed 4 months ago
1
set time limit to 2hrs for genefuse

#51 ramsainanduri closed 4 months ago
0
Dsl2 hg38 ref fix

#50 ramsainanduri closed 5 months ago
0
Illegal division by zero at find_contaminant.pl

#49 ramsainanduri closed 5 months ago
0
Fix HG38 (masked) reference files to support all the profiles

#48 ramsainanduri closed 5 months ago
0
PGX Module: CSV and Shell Script Creation

#47 ramsainanduri closed 5 months ago
0
Generate a CSV input file for the Pharmacogenomics (Pgx) pipeline within the Solid profile.

#46 ramsainanduri closed 5 months ago
0
Tests for different subworkflows

#45 sailepradh opened 7 months ago
0
Increment SampleId by one only upon an exact match in the database.

#44 ramsainanduri closed 7 months ago
0
Increment SampleId by one only upon an exact match in the database.

#43 ramsainanduri closed 6 months ago
0
Appending groupID with 'p' for the paired vcf

#42 ramsainanduri closed 7 months ago
3
Append 'p' to Group ID in Paired Mode for Segregation of Sample VCF Files

#41 ramsainanduri closed 7 months ago
0
Bugfix: fixed publishDir in the configs for the output files with mul…

#40 ramsainanduri closed 7 months ago
0
Bug: Publishing Files Fails When Multiple Patterns Are Defined

#39 ramsainanduri closed 7 months ago
0
Modularized configs and readable code structure

#38 ramsainanduri closed 8 months ago
5
CNV import to coyote as JSON. Pythonize the import

#37 ViktorHy closed 2 months ago
0
DSL2 live version for PARP

#36 ViktorHy closed 7 months ago
0
vcfanno_anno BUG FIX:

#35 ramsainanduri closed 8 months ago
1
Markgermline rank

#34 ViktorHy closed 1 month ago
2
freebayes multi-allelic variants dissapear

#33 ViktorHy opened 8 months ago
1
Bug: fix versions for vcfanno_linux64

#32 ramsainanduri closed 8 months ago
0
Fix merging cnvs

#31 ViktorHy closed 8 months ago
1
VEP produces bugged CSQ-fields

#30 ViktorHy opened 9 months ago
0
save all qc in json

#29 ViktorHy opened 9 months ago
1
Melt updates const

#28 ViktorHy closed 8 months ago
1
Add stub blocks

#27 ramsainanduri closed 9 months ago
0
Added Stubs and Versions

#26 ramsainanduri closed 9 months ago
1
Create a json import of CNVs

#25 ViktorHy opened 9 months ago
2
Automatic download/install singularity

#24 ViktorHy opened 9 months ago
1
Fix merging cnvs

#23 ViktorHy closed 9 months ago
0
Testing suites

#22 ViktorHy opened 9 months ago
0
Output versions

#21 ViktorHy closed 9 months ago
1
Complete modulization of configs

#20 ViktorHy closed 7 months ago
1
Rename workflows and subworkflows

#19 ViktorHy closed 7 months ago
1
Look into CNV-merge through SVDB

#18 ViktorHy closed 9 months ago
1