hartwigmedical hmftools issues

hartwigmedical / hmftools

Various algorithms for analysing genomics data

GNU General Public License v3.0

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Advice needed in regards to the `gridss_blacklist` within `hmf_dna_pipeline_resources.38_v5.34.tar.gz`

#573 Teezi closed 5 hours ago
1
GRIPSS running issue

#572 Teezi closed 5 hours ago
1
INFRA-499 Backport db_sample argument for CIDER and TEAL loader

#571 mdenburger closed 6 days ago
0
java.lang.ClassCastException: class java.util.ArrayList cannot be cast to class java.lang.String

#570 lipikakalson opened 1 week ago
2
ACTIN-1057: Filter NaN likelihoods from CUPPA when converting in ORANGE

#569 kduyvesteyn closed 1 week ago
0
Length neoepitopes

#568 p-levy closed 1 week ago
2
Switch to MIT license

#567 kduyvesteyn closed 1 week ago
1
Exception in thread "main" java.lang.IllegalArgumentException: No enum constant com.hartwig.hmftools.common.genome.chromosome.HumanChromosome._GL000217.1

#566 JiwonShon opened 2 weeks ago
1
Linx visualiser error

#565 mich-chan opened 2 weeks ago
0
ACTIN-1010: Add workaround for some orange to isofox cancer type mappings

#564 kduyvesteyn closed 2 weeks ago
0
CNV and LOH analysis for TSO500

#563 ningb opened 3 weeks ago
0
ACTIN-1007: Set context to "Unknown" for promiscuous enhancer targets

#562 kduyvesteyn closed 2 weeks ago
0
ACTIN-999: Remove pre-LILAC v1.6 check from ORANGE

#561 kduyvesteyn closed 3 weeks ago
0
ACTIN-995: Add immune escape analysis to ORANGE datamodel and report

#560 kduyvesteyn closed 3 weeks ago
1
DEV-4021: Patient-DB adjustments for Peach Java

#559 DFKoetsier closed 1 month ago
0
Sigs for Structural Variants

#558 amarinderthind closed 1 month ago
1
CNV results from purple

#557 zhaowsong closed 1 month ago
6
Driver Catalog File missing

#556 zhaowsong closed 1 month ago
3
raw copy numbers

#555 Pranav-Garg opened 1 month ago
4
Patient db 5.34

#554 mvanniekerkHartwig closed 1 month ago
0
INFRA-459 Add optional purple DB sample argument to overwrite the sample name in the database

#553 mvanniekerkHartwig closed 1 month ago
0
PatientDB: restore index prefix length of cpctEcrf.itemValue column

#552 mdenburger closed 1 month ago
2
Update README_ONCOANALYSER.md

#551 scwatts closed 2 months ago
0
Replication Timing in the .linx.svs files

#550 tillyRigby555 closed 1 month ago
1
Isofox and Very Polymorphic Human Genes

#549 DarioS closed 2 months ago
6
DEV-3784: Expand Liftover in Compar

#548 DFKoetsier closed 1 month ago
0
NullPointerException for SageApplication

#547 Tina04021997 closed 2 months ago
2
Mkcmkc bam to fastq

#546 charlesshale closed 2 months ago
0
Problem running Lilac

#545 vaksmaz closed 2 months ago
1
Issue configuring Lilac

#544 vaksmaz closed 2 months ago
1
ACTIN-808: Add PurpleTranscriptImpact.reported flag to orange datamodel

#543 kzuberihmf closed 2 months ago
4
Mkcmkc sage dev2

#542 charlesshale closed 2 months ago
1
Add htsget support for SAGE

#541 brainstorm opened 2 months ago
2
SvPrep Depth Annotator missing VCF when no SVs detected

#540 scwatts closed 1 month ago
2
ACTIN-551: Add maxCopyNumber to PurpleGeneCopyNumber datamodel in orange datamodel

#539 dvanbeek closed 2 months ago
0
FYI: copynumber package removed from Bioconductor >=3.18

#538 toddajohnson opened 3 months ago
0
INFRA-347: Support unusual esophageal DOID configuration in cohort mapping

#537 kduyvesteyn closed 3 months ago
0
Update README_ONCOANALYSER.md

#536 scwatts closed 3 months ago
0
Skip faulty CIGARs instead of crashing

#535 Pranav-Garg closed 3 months ago
5
DEV-3771: Bam-tools metrics ignores some reads for WgsMetrics

#534 DFKoetsier opened 3 months ago
0
NullPointerException using teal

#533 elicj01 closed 1 month ago
3
i cannot find GermlineHetPon.37.vcf.gz in v5_34 resources

#532 nan5895 closed 3 months ago
1
TEAL error: Exception in thread "main" java.lang.IllegalArgumentException: Comparison method violates its general contract!

#531 JeanetteCKittel closed 4 months ago
1
mappability.hdr not found + stitching resource files

#530 mich-chan closed 3 months ago
1
AUS-229: CUPPA cohort level feature extraction

#529 luan-n-nguyen closed 3 months ago
0
ACTIN-642: Improve CUPPA output layout

#528 cbruel closed 3 months ago
4
DEV-3767: Update test run in Orange resource files to 5.34

#527 DFKoetsier closed 4 months ago
1
DEV-3766: Fix germline MVLH table in PDF

#526 DFKoetsier closed 4 months ago
1
Update README_ONCOANALYSER.md

#525 scwatts closed 4 months ago
0
Latest version of PURPLE is not working with MultiQC

#524 insilicool closed 4 months ago
1