Giters
CRG-CNAG
/
CalliNGS-NF
GATK RNA-Seq Variant Calling in Nextflow
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9
Issues:
26
Forks:
53
CRG-CNAG/CalliNGS-NF Issues
ERROR: Input files reference and features have incompatible contigs
Updated
2 years ago
Operator `phase` is deprecated
Updated
2 years ago
Process `ASE_KNOWNSNPS (SAMPLE123XYZ)` terminated with an error exit status (2) (More then one variant context at position: chr3:XXXXXXX)
Updated
2 years ago
Comments count
2
will there be a nf of dna variant calling which need paired samples
Updated
3 years ago
Documentation issue?
Updated
3 years ago
Comments count
2
denylisted genome file
Updated
3 years ago
Could not build fai index genome.fa.fai
Updated
3 years ago
The on-the-fly two-pass option could be used to avoid the genome regeneration step
Closed
3 years ago
Comments count
3
mm39 variants / black list
Updated
3 years ago
Comments count
4
Whether do not generate star index if provide directly?
Updated
3 years ago
Comments count
1
could not execute mkdir
Closed
4 years ago
Comments count
1
Process POST_PROCESS_VCF failes when order of chromosomes in result.DP8.vcf differs from that in the GRCm38/Annotation/Variation/Mus_musculus.vcf
Updated
4 years ago
Reading single end reads
Updated
4 years ago
Comments count
4
The genomeDir dir name is confusing
Closed
4 years ago
containerOverrides for AWS BATCH
Updated
4 years ago
Comments count
1
picard.jar not found
Closed
4 years ago
Comments count
1
GATK4 branch does not require separate Picard
Closed
4 years ago
Comments count
3
samtools: command not found
Closed
4 years ago
Comments count
3
Implement support for GATK4
Closed
4 years ago
Comments count
17
suggest adding docker runOptions to nextflow.config
Closed
4 years ago
Comments count
1
Cannot locate GATK.jar file
Closed
4 years ago
Comments count
1
Error: Unable to access jarfile /scratch/oknjav001/transcriptomics/proteogenomics/variabtcalling/gatk/gatk3.7/GenomeAnalysisTK.jar
Closed
4 years ago
Comments count
1
Using Single end data
Closed
5 years ago
Comments count
5
Error in SplitNCigarReads step
Closed
6 years ago
Comments count
3
Variant calling step failing when using process scratch
Closed
7 years ago
Comments count
1
Typo in the title of the flow-chart picture.
Closed
7 years ago