SciLifeLab / Sarek

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

https://nf-co.re/sarek

SciLifeLab/Sarek Issues

Look into MultiQC report for multi patients TSV
Closed 4 years ago1
Should we use -Y option for bwa mem?
Closed 4 years ago1
ASCAT with WES
Closed 4 years ago5
Add variants comparison between multiple T/N pairs from the same patient.
Closed 4 years ago1
markduplicates will fail when no lane information is given in sample.tsv
Closed 4 years ago2
error running the test
Closed 4 years ago4
Errors running sarek with Nextflow 19.07 - command 'ps' not found
Closed 5 years ago13
Look into using spark for gatk
Closed 5 years ago5
ERROR: resolved path doesnt match with open path
Closed 5 years ago17
Mix SIngle end and Paired end data
Closed 5 years ago2
Strange VCFTools graphs in MultiQC report
Closed 5 years ago1
containerOverrides for AWS BATCH nextflow
Closed 5 years ago4
Huge problem with pipeline on Happlotype caller
Closed 5 years ago1
BWA map error
Closed 5 years ago4
No variants IDs annotated
Closed 5 years ago1
RunVcftools fails while annotating manta vcf
Closed 5 years ago1
fastqc not running on soft linked files
Closed 5 years ago1
Check slurm settings in uppmax-slurm.config
Closed 5 years ago
Questions about Strelka -BP
Closed 5 years ago2
Max CPUs Workstation Utilization
Closed 5 years ago5
Parallelisation of CreateRecalibrationTable
Closed 5 years ago3
Should we include CADD annotations?
Closed 5 years ago2
Missing hints for capital letters required
Closed 5 years ago1
Update to VEP 96
Closed 5 years ago2
Target Bed for HaplotypeCaller
Closed 5 years ago13
Cannnot annotate using CADD
Closed 5 years ago1
Annotation with both SnpEff and VEP
Closed 5 years ago1
RunVCFTools and RunBcftoolsStats are run twice for the same input
Closed 5 years ago2
VEP only annotates Tumor samples
Closed 5 years ago5
Add ControlFREEC
Closed 5 years ago2
Provide ASCAT GC File via iGenomes
Closed 5 years ago3
Reference for ASCAT required even when not calling with ASCAT
Closed 5 years ago2
ASCAT loci for download link timeout
Closed 5 years ago2
Error executing process ConcatVCF
Closed 5 years ago8
Panel of Normals with Mutect2
Closed 5 years ago12
fq.gz extension
Closed 5 years ago2
Coverage 0.0X on whole exome sequencing data
Closed 5 years ago3
Update GATK TO 4.1.1.0 and include CNN
Closed 5 years ago1
Warning - access to undefined parameter related to annotation cache
Closed 5 years ago5
Specifying interval for targeted sequencing
Closed 5 years ago2
ERROR ~ For input string: "status"
Closed 5 years ago4
Error with RunVcftools on a Manta VCF
Closed 5 years ago2
Snpeff for SV annotation?
Closed 5 years ago2
Error with Manta in SomaticVC.nf
Closed 5 years ago8
Improve VEP runtime
Closed 5 years ago
Make Sarek work with Conda
Closed 5 years ago4
Error with annotate.nf
Closed 5 years ago3
Mutect2 vcfs improperly formatted
Closed 5 years ago
FastQC hangs forever on Travis CI
Closed 5 years ago1
Error: "TMP_DIR is not a recognized option" from CreateRecalibrationTable
Closed 5 years ago1