# Sarek Issue Classification (Clean) **Date:** 2026-02-16 | **Open Issues:** 238 ## Summary | Category | Count | | ------------------------------- | ------- | | Quick Win | 13 | | Syntax Compliance | 2 | | Optimization (Runtime) | 11 | | Giant Genomes | 2 | | Bug: Join Mismatch / Dataflow | 7 | | Bug: Input / Samplesheet | 13 | | Bug: CRAM / BAM Output | 6 | | Bug: Container | 3 | | Tool: ASCAT | 11 | | Tool: CNVkit | 15 | | Tool: Control-FREEC | 3 | | Tool: Mutect2 | 4 | | Tool: GATK / HaplotypeCaller | 32 | | Tool: VEP / snpEff | 13 | | Tool: Sentieon | 6 | | Tool: DeepVariant / DeepSomatic | 5 | | Tool: Strelka | 3 | | Tool: Manta | 2 | | Tool: LoFreq | 2 | | Tool: DragMap | 2 | | Tool: TIDDIT | 1 | | Tool: BCFTools | 4 | | Resume / Restart | 2 | | UMI | 6 | | Documentation | 9 | | Testing / CI | 5 | | Intervals / BED | 4 | | Error Messages / UX | 4 | | Reference Files / Genome | 9 | | New Tool Requests | 7 | | Preprocessing / Alignment | 8 | | Platform / Infrastructure | 4 | | QC Enhancements | 3 | | Tool: Freebayes | 2 | | Tool: MSISensor | 1 | | MultiQC / Reporting | 1 | | Feature Backlog | 13 | | **Total** | **238** | --- ## Quick Win (13) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------- | ----- | | 2082 | Fixed the missed rename in the annotate.config to be `snv_consensus_calling | - | 60d | | 2034 | No automatic email recieved after successful completion of pipeline in Sare | bug | 121d | | 2022 | Unclear docu on non-human genomes | bug, docs | 125d | | 2012 | Move tests/config/bcfann_test_columns.txt to test-datasets repo | - | 136d | | 1946 | GATK Joint Germline Variant Calling - FilterVariantTranches - Documentation | bug | 201d | | 1537 | Check if any empty folders are created | bug | 634d | | 1437 | Minor: empty output folder for fastp created (see aws ful size tests) | bug | 703d | | 1427 | Update docs: Haplotypecaller is fine without BQSR (got nothing to do with d | bug | 718d | | 1282 | The pipeline should fail early when --no_intervals is used with joint germl | bug | 858d | | 1281 | Readme uses bith light and dark logo at all times | bug | 858d | | 1187 | Improvement: make --tools case insensitive | enhancement | 912d | | 877 | Put annotation in same output structure, regardless of -step entry point | enhancement | 1172d | | 845 | Use -cancer for snpeff samples | enhancement | 1187d | --- ## Syntax Compliance (2) | # | Title | Labels | Age | | ---- | -------------------------------------------------------------- | ----------- | ---- | | 1976 | Plan for migrating sarek to accordance with Nextflow LS | enhancement | 158d | | 1250 | Stop ignoring parameter validation, lenient mode is sufficient | - | 878d | --- ## Optimization (Runtime) (11) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------- | ----- | | 2132 | Cram still beign created in the "work folder" even if I don't need to it be | - | 5d | | 2023 | Only calculate DICT when needed | enhancement | 125d | | 1840 | Why is the `ENSEMBLVEP_VEP` process not ran on chunks? | enhancement | 330d | | 1332 | Java applications request too much memory | bug | 823d | | 1141 | Pass on the number of tumor samples per patient | enhancement | 958d | | 1127 | Sarek copies dbSNP for each invocation of HaplotypeCaller | bug | 970d | | 1121 | Optimisation: Drop samtools index processes | enhancement | 971d | | 1076 | Feature: Pipe bamtofastq conversion for speed up | enhancement | 985d | | 1072 | Revisit resource requests | - | 986d | | 1038 | Mosdepth in sarek runs default with --fast-mode. Could this be made configu | enhancement | 997d | | 880 | Automatic identification of callable regions to parallelize BQSR and varian | enhancement | 1168d | --- ## Giant Genomes (2) | # | Title | Labels | Age | | ---- | -------------------------------------- | ---------------- | ----- | | 1018 | Please add CSI indexing | enhancement | 1012d | | 900 | tabix fails for large chromosome sizes | bug, enhancement | 1151d | --- ## Bug: Join Mismatch / Dataflow (7) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | -------- | ---- | | 2136 | Error "Detected join operation duplicate emission on left channel" when usi | - | 4d | | 2110 | Join mismatch error | moreinfo | 26d | | 2078 | Pipeline Error: Join mismatch for the following entries: | bug | 66d | | 2064 | Detected join operation duplicate emission on right channel | bug | 75d | | 2036 | Bug Report — Join mismatch when using mutect2 tool | bug | 117d | | 1790 | Join mismatch/DataflowVariable assignment error | bug | 377d | | 1455 | Additional documentation for specifying ext.args for Mutect2 to avoid join | docs | 683d | --- ## Bug: Input / Samplesheet (13) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------------------------- | ----- | | 1658 | Wrong sample names in multiqc general table | bug | 514d | | 1655 | A USER ERROR has occurred: Bad input: Sample $name is not in BAM header: [. | bug | 515d | | 1629 | Avoid misleading error messages concerning sample-sheets | bug | 538d | | 1528 | Different sample name handling causes issues with merging | bug | 640d | | 1503 | same sample name over multiple patient doest not fail input schema validati | bug, samplesheet | 650d | | 1451 | Non-unique of `sample` values across several patients causes name clashes | bug, input validation | 688d | | 1293 | Samplesheets with more normal-samples per patient pass nf-validation | bug, input validation | 846d | | 1279 | Parameter validation doesn't catch of unzipped vcf is supplied | bug | 859d | | 1276 | lane should be optional if unique | enhancement | 860d | | 1255 | flowcellLaneFromFastq cannot handle weird fastq header | bug | 873d | | 1152 | Make patient optional in the samplesheet | enhancement | 950d | | 989 | Add optional capability of adding the BED file into samplesheet | enhancement | 1046d | | 97 | Check BED compatibility | enhancement, input validation | 2211d | --- ## Bug: CRAM / BAM Output (6) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------------------- | ---- | | 2086 | Enable "save_output_as_bam: True“ for parabricks | enhancement, parabricks | 48d | | 1919 | Invalid CRAM file: some paired and mapped reads missing from recalibrated C | bug | 246d | | 1914 | Work with split chromosome and cram | bug | 257d | | 1894 | Missing conversion from bam to cram when starting from "--step prepare_reca | question | 277d | | 1424 | Allow cram in mapping step | CRAM | 722d | | 1182 | Managing CRAM compression level | enhancement | 913d | --- ## Bug: Container (3) | # | Title | Labels | Age | | ---- | ------------------------------------------ | ------ | ---- | | 1519 | Sarek test run unable to find docker image | bug | 646d | | 1362 | Check docker.runOptions for spark | - | 788d | | 1233 | Question regarding sarek dockers : | - | 885d | --- ## Tool: ASCAT (11) | # | Title | Labels | Age | | ---- | -------------------------------------------------------------------------- | ------------- | ----- | | 2089 | ASCAT Exome processing steps incorrect for hg38 | bug | 38d | | 1837 | ASCAT not running in sarek | bug | 335d | | 1526 | WES files provided by ascat author | docs | 640d | | 1512 | Copy-Number Enhancements - Ascat joint calling | enhancement | 649d | | 1510 | Copy-Number Enhancements - Ascat penality | enhancement | 649d | | 1432 | ASCAT WES reference resources | enhancement | 710d | | 1375 | improve documentation to point out that when using ASCAT and the Format in | bug | 762d | | 1346 | No parameter for "penalty" in ASCAT segmentation | enhancement | 807d | | 1323 | Error with ASCAT | bug | 830d | | 1176 | Add Ascat tumor-only & targeted mode | enhancement | 922d | | 1020 | Error while running ASCAT | bug, moreinfo | 1010d | --- ## Tool: CNVkit (15) | # | Title | Labels | Age | | ---- | ------------------------------------------------------------------- | --------------------- | ----- | | 2000 | CNVKit Tutorial / Improved Documentation / Track issues with CNVkit | enhancement | 139d | | 1981 | Improve cnvkit tumor_only mode | - | 157d | | 1895 | Bump samtools in cnvkit | - | 272d | | 1625 | `cnvkit` output files are missing | bug | 545d | | 1610 | CNVKIT doesn't accept \*.list format interval files | bug, input validation | 562d | | 1606 | cnvkit reference titling broken | bug | 564d | | 1591 | base.conf does not override module's process.label for CNVKIT_BATCH | bug | 584d | | 1562 | Pooled normals for CNVkit | enhancement | 613d | | 1322 | How to output allele-specific copy number in CNVkit? | enhancement | 830d | | 1292 | CNVKIT - Export cns file into seg format for IGV | - | 850d | | 1251 | Output files for CNVkit incorrect | bug | 878d | | 1234 | Add gene annotation on cnvkit for WGS (--annotate) | enhancement | 885d | | 972 | Help with understanding & manipulate CNVkit output | docs | 1063d | | 924 | CNVkit reference issue for WGS tumor-only samples | bug | 1115d | | 863 | Improve CNVKit | enhancement | 1180d | --- ## Tool: Control-FREEC (3) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | --------------------- | ----- | | 1449 | Sarek possibly supplying the wrong number of args for CONTROLFREEC_ASSESSSI | bug | 694d | | 1376 | control-freec throws an error when running WES data in tumor-only mode beca | bug | 762d | | 808 | controlfreec with multiple ploidy values results in plotting error | bug, input validation | 1200d | --- ## Tool: Mutect2 (4) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------------------------- | ---- | | 1883 | Enable Mutect2 force-calling using --alleles flag | enhancement, good first issue | 289d | | 1766 | mutect2-realigned .bam output | enhancement | 404d | | 1546 | FILTERMUTECTCALLS is not run for tumor-only samples when there is no germli | bug | 629d | | 1049 | Allow genotyping germline sites with Mutect 2 | enhancement | 992d | --- ## Tool: GATK / HaplotypeCaller (32) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | --------------------- | ---------------- | ----------- | ----- | | 2140 | Constant OOM error for GetPileupSummaries on EC2 | bug | 3d | | 2131 | OOM error for GetPileupSummaries on EC2 | question | 5d | | 2118 | Silent failure in FASTQ_PREPROCESS_GATK for multi-lane samples (no outputs | bug | 14d | | 2097 | GATK BaseRecalibrator interval usage affects variant calling | question | 32d | | 2040 | 401 Unauthorized error from Singularity gatk | bug | 115d | | 1949 | Potentially incompatible outputs are generated with BAM output and Spark Ma | bug | 194d | | 1918 | GATK4_MARKDUPLICATES not respecting --TMP_DIR | bug | 248d | | 1901 | GATK GenotypeGVCFs memory issue when including non-variant-sites and using | - | 265d | | 1893 | Add option to run GATK FilterByOrientationBias | enhancement | 278d | | 1880 | GATK tooling update to fix Bug in Markduplicates | - | 291d | | 1870 | GATK joint variant calling with option --include-non-variant-sites fails du | enhancement | 304d | | 1822 | single germline sample VCF quality control | enhancement | 342d | | 1772 | How to prevent ApplyBQSR from passing intervals to prevent it from dropping | community-feedback | 396d | | 1722 | the vcf file from haplotypecaller was not annotated by snpeff and vep | question | 470d | | 1645 | error running BQSR: cannot remove tmp file | bug | 529d | | 1617 | GATK4_HAPLOTYPECALLER not running in parallel | bug | 555d | | 1616 | Restart from step variantcalling fails on haplotypecaller | bug | 556d | | 1598 | GATK4_MARKDUPLICATES : Not a valid path value type: java.util.ArrayList | bug | 579d | | 1586 | Add an option to optionally use the GATK VariantFiltration instead of VQSR | enhancement | 586d | | 1434 | GenomicsDBImport fails when no_intervals is set to true | bug, input validation | 709d | | 1389 | Default Bed file GATK.GRCh37 contains timings: remove those | bug | 744d | | 1356 | ngscheckmate_bed is set incorrectly for GATK.GRCh37 | bug | 795d | | 1329 | haplotypecaller output unusual behavior without dbsnps/known-sites | bug | 824d | | 1146 | Better "error handling" around FilterVariantTranches | enhancement | 954d | | 959 | Use GATK small_exac_common_3.hg38.vcf.gz as default germline_resource | enhancement | 1080d | | 923 | joint genotyping optimal strategy | help wanted | 1117d | | 911 | Add `GATK4_CALIBRATEDRAGSTRMODEL` | enhancement | 1126d | | 908 | Add option for outputting gvcfs instead of vcfs | enhancement | 1131d | | 902 | Reference Allele Error on dbSNP on step HaplotypeCaller CNN1 | docs | 1144d | | 899 | CalculateContamination table needs to be sorted | - | 1154d | | 881 | --genome flag, allow for AWS iGenomes GATK.b37 | enhancement | 1167d | | 868 | Population calling | joint calling | ensemble calling | enhancement | 1178d | --- ## Tool: VEP / snpEff (13) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------- | ----- | | 1980 | Snpeff databases can not be downloaded | bug | 157d | | 1948 | VEP Cache - AWS S3 Access ID Error | bug | 195d | | 1854 | Missing c. and p. Position in VEP Annotation & OMIM/RefSeq Intersection Iss | bug | 319d | | 1691 | `vep_loftee` doesn't add the expected columns to `INFO/CSQ` | bug | 482d | | 1654 | use custom snpeff database, such as Candian.aruis | bug | 517d | | 1549 | Please add VEP plugins (Conservation and Condel) | enhancement | 626d | | 1355 | Allow to specify a local config file for snpEff | enhancement | 796d | | 1354 | Allow for snpEff db without versions | enhancement | 796d | | 1326 | Misleading info in error message concerning invalid path to VEP-cache | bug | 825d | | 1265 | AlphaMissense VEP Plugin Integration | enhancement | 867d | | 984 | Need to document snpeff_cache/vep_cache clashes with snpeff_version/vep_ver | enhancement | 1053d | | 879 | Variant annotation for non-coding genes | enhancement | 1171d | | 878 | annotation enhancement | enhancement | 1172d | --- ## Tool: Sentieon (6) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ------------------------------- | ---- | | 1869 | Refactor Sentieon preprocessing Modules into Subworkflow | sentieon | 307d | | 1865 | Remove license file support for Sentieon | sentieon | 311d | | 1548 | Remove duplicated config-snippet for SENTIEON_GVCFTYPER | sentieon, refactor | 626d | | 1480 | Missing input validation: Error handle for sentieon-dedup with non-sentieon | bug, input validation, sentieon | 663d | | 1399 | Sentieon bundle file | bug, sentieon | 738d | | 1296 | ContaminationAssessment in the Sentieon-subworkflows TNseq and TNscope? | enhancement, sentieon | 845d | --- ## Tool: DeepVariant / DeepSomatic (5) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------- | ----- | | 2081 | nf-core pipelines download fails: missing DeepVariant container (offline in | bug | 61d | | 1583 | DeepVariant params addition request: | enhancement | 587d | | 1440 | Add DeepSomatic to the Sarek Pipeline | - | 699d | | 1066 | Future proof Deepvariant output | - | 986d | | 682 | Deepvariant requires additional cli option for recalibrated BAM files | bug | 1304d | --- ## Tool: Strelka (3) | # | Title | Labels | Age | | ---- | ----------------------------------------------------------------- | --------------------- | ----- | | 2127 | Strelka2 stuck at 99% for over 24 hours (reopen) | - | 8d | | 1306 | Strelka requires `.crai` files to match format `PREFIX.cram.crai` | bug, input validation | 836d | | 1023 | Problem running Strelka due to Python version difference | bug | 1007d | --- ## Tool: Manta (2) | # | Title | Labels | Age | | ---- | --------------------------------------------------------- | ------ | ---- | | 1611 | ERROR > SAREK_BAM_VARIANT_CALLING_GERMLINE (MANTA) | bug | 561d | | 1387 | Manta (germline) terminated with an error exit status (1) | bug | 746d | --- ## Tool: LoFreq (2) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ------------- | ---- | | 1963 | LoFreq doesn't run even when tumor/normal status is omitted | bug, question | 166d | | 1588 | Add lofreq call-parallel (tumor-only) and lofreq somatic as variant callers | enhancement | 584d | --- ## Tool: DragMap (2) | # | Title | Labels | Age | | ---- | --------------------------------------------- | ------------- | ---- | | 1555 | DRAGMAP_Alignment_error | bug, moreinfo | 615d | | 1445 | DragMap fails if --trim_fastq flag is enabled | bug | 697d | --- ## Tool: TIDDIT (1) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ------ | ---- | | 1441 | TIDDIT_SV produces `*.tiddit.ploidies.tab` but not `*.tiddit.vcf`, timing o | bug | 698d | --- ## Tool: BCFTools (4) | # | Title | Labels | Age | | ---- | ---------------------------------------------------------------------- | ----------- | ----- | | 2085 | Question: Advanced filtering with --bcftools_filter_criteria parameter | - | 59d | | 885 | Replace the locale module add_info_to_vcf with bcftools | enhancement | 1166d | | 826 | BCFTools use region/target file | enhancement | 1193d | | 699 | Pass target-bed-file to bcftools/stats? | enhancement | 1294d | --- ## Resume / Restart (2) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ------ | ---- | | 2042 | How to skip rerunning tasks that have already been completed when using the | bug | 108d | | 1615 | Restart from step variantcalling fails on NGScheckmate | bug | 556d | --- ## UMI (6) | # | Title | Labels | Age | | ---- | ---------------------------------------------------- | ----------- | ----- | | 2114 | UMI-aware Sarek | question | 18d | | 1719 | Provide default UMI/trimming library specific values | enhancement | 472d | | 1714 | Tutorial: UMI | enhancement | 473d | | 1316 | Fix UMI-link | bug | 831d | | 907 | Support for Illumina ORA format | enhancement | 1131d | | 871 | Support for UMI FASTQ | enhancement | 1175d | --- ## Documentation (9) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ------------------------------ | ----- | | 2107 | Create a contributors guide with specifics for this pipelines | - | 26d | | 1861 | Q: how to deal with the fact that msisensor pro is free for non-commercial | - | 317d | | 1717 | Tutorial: long reads analysis | enhancement | 473d | | 1713 | Tutorial: CNV calling | enhancement, help wanted | 473d | | 1704 | Proposals for Sarek Tutorials on use-cases | help wanted, docs, testing | 475d | | 1643 | Sarek How Tos | - | 530d | | 1576 | Test and document that Sarek can handle input-samplesheets with mixed sampl | enhancement, docs, samplesheet | 600d | | 852 | add more info about which process are affected by --wes | enhancement, docs | 1186d | | 848 | Provide typical usage of --tools | enhancement | 1187d | --- ## Testing / CI (5) | # | Title | Labels | Age | | ---- | -------------------------------------------------------------------- | ------------------------ | ---- | | 2090 | Enhance tests/variantcalling_all with all tools | - | 34d | | 1958 | Use nft-csv to better test csv files | enhancement | 180d | | 1860 | Duplicate test-data inputs | testing | 317d | | 1699 | Get a full nf-test report in cis | enhancement, help wanted | 475d | | 1544 | Add more intricate CI tests to verify multiple/single lanes run well | testing | 629d | --- ## Intervals / BED (4) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | ----------------- | ----- | | 1523 | port CREATE_INTERVALS_BED to nf-core/modules | enhancement | 641d | | 1148 | Intervals BED file processing: remove headers and validate any timing infor | enhancement | 952d | | 934 | Perform a compatibility check between bed file specified at --targets and r | enhancement | 1108d | | 534 | [BUG] Scatter/gather of intervals uses misleading filename (content is fine | bug, Low priority | 1384d | --- ## Error Messages / UX (4) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------- | ----------------------------- | ---- | | 1978 | Re-work all error messages | - | 158d | | 1685 | No status is 0 - but contains tumor only sample error message | bug, help wanted | 492d | | 1435 | Add some docs crosslinking the warning about kubernetes and GLS | - | 709d | | 1416 | Better error message for empty fastq files | enhancement, input validation | 725d | --- ## Reference Files / Genome (9) | # | Title | Labels | Age | | ---- | --------------------------------------------------------------------------- | --------------------- | ----- | | 2072 | Prepare reference before run pipeline | bug | 68d | | 1741 | Check that GZI index provided if using a gzipped FASTA | enhancement, moreinfo | 443d | | 1650 | Add pattern for all reference files | enhancement | 521d | | 1649 | error when use custom reference | bug | 521d | | 1308 | Be consistent with the meta map for the reference files | - | 835d | | 1253 | Error out when user provides both custom genome files (fasta, fai, dict, et | enhancement | 874d | | 995 | Check & update reference files | enhancement | 1039d | | 829 | Add T2T reference | enhancement | 1193d | | 712 | BWA index isn't coppied over with using save-reference option | bug, Azure | 1273d | --- ## New Tool Requests (7) | # | Title | Labels | Age | | ---- | ------------------------------------------------ | ------------------------------- | ----- | | 2056 | Inquiry about integrating Octopus variant caller | enhancement | 90d | | 2030 | varlociraptor issues | - | 122d | | 1950 | New variant caller VarScan | enhancement | 191d | | 1630 | AGeNT | enhancement | 538d | | 875 | Add IGV visualization for alignment files | enhancement | 1173d | | 95 | Community feedback: consider other tools | enhancement, community-feedback | 2211d | Note: DeepSomatic (#1440) already tracked under Tool: DeepVariant/DeepSomatic. --- ## Preprocessing / Alignment (8) | # | Title | Type | Labels | Age | | ---- | --------------------------------------------------------- | ----------- | ----------- | ----- | | 1889 | bwa mem does not align to ALT chromosomes | Bug | - | 282d | | 1492 | Error creating symlinks to BWAIndex | Bug | bug | 656d | | 1452 | bwa index can not build | Bug | bug | 685d | | 1443 | No reads for mitochondrial chromosome after recalibration | Bug | bug | 697d | | 838 | Add samtools markdup as duplicate marking alternative | Enhancement | enhancement | 1188d | | 1367 | sambamba/markdup | Enhancement | enhancement | 780d | | 830 | Customize Preprocessing based on each tool | Enhancement | enhancement | 1192d | | 922 | Port local sarek subworkflows to modules | Enhancement | enhancement | 1117d | --- ## Platform / Infrastructure (4) | # | Title | Labels | Age | | ---- | ---------------------------------------------- | ----------- | ---- | | 1853 | Sarek goes GPU - parabricks integration | - | 320d | | 1843 | ARM pipeline run end to end | - | 328d | | 1447 | ERROR Timeout waiting for connection from pool | bug | 696d | | 1446 | meta-sarek: One pipeline to rule them all | enhancement | 696d | --- ## QC Enhancements (3) | # | Title | Labels | Age | | ---- | ---------------------------------------------------------- | ----------- | ----- | | 1379 | Run BAM QC after alignment | enhancement | 759d | | 944 | Add target capture performance via Picard HsMetrics module | enhancement | 1094d | | 962 | Support for FilterSamReads | enhancement | 1075d | --- ## Tool: Freebayes (2) | # | Title | Labels | Age | | ---- | ----------------------------------------------------- | --------------------- | ----- | | 1900 | Make Freebayes --min-alternate-fraction more explicit | enhancement, moreinfo | 265d | | 453 | gvcf option for freebayes | enhancement | 1551d | --- ## Tool: MSISensor (1) | # | Title | Labels | Age | | ---- | --------------------------------- | ----------- | ---- | | 1599 | Add msisensor-pro tumor-only mode | enhancement | 578d | --- ## MultiQC / Reporting (1) | # | Title | Labels | Age | | ---- | --------------------------------------------------- | ------ | ---- | | 1926 | multiqc report contents when using --step parameter | - | 242d | --- ## Feature Backlog (12) Remaining enhancements and bugs not fitting neatly into other categories. | # | Title | Labels | Age | | ---- | -------------------------------------------------------- | ----------- | ----- | | 2015 | Pipeline interrupts immediately after launching | bug | 136d | | 2006 | vcftools bug interrupts execution under --joint_germline | bug | 138d | | 1716 | Check if flowcell id is uniform in a fastq file | enhancement | 473d | | 1715 | Add library metadata and extend read group info | enhancement | 473d | | 1637 | A question with hg19 | question | 535d | | 1429 | chrFiles/GCcontentProfile error (Control-FREEC related) | bug | 713d | | 1142 | Time course sampling analysis | enhancement | 957d | | 1125 | Adding more keys in INFO and FORMAT fields | enhancement | 970d | | 1124 | Joint calling with mpileup | enhancement | 970d | | 1029 | Stop Sarek early on low quality input | enhancement | 1003d | | 755 | Start pipeline from --joint_germline step | enhancement | 1244d | | 523 | Haplotype aware effect prediction | enhancement | 1397d | | 495 | Tumor mutational burden (TMB) scoring | enhancement | 1440d | | 98 | Sex determination option | enhancement | 2211d |