Description of the bug
Hello,
I want to call variants from RNA-seq data that I was provided in BAM format. I have already mark the duplicates, fixmate, fixed readgroups, fixed header information to work with the refseq format and sorted the reads. ValidateSamFile doesnt return any issues. This was able to solve all errors up until the current step: GATK4_MERGEVCFS.
I get the following error: java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator
The full error log:
nextflow.log
Command used and terminal output
nextflow run nf-core/rnavar -profile docker --input rnavar_test.csv --genome GRCh38 --skip_baserecalibration true --outdir rnavar -w /mnt/data/Till/work/
Relevant files
No response
System information
Linux VM
(I run sarek on this same VM without problems)
Description of the bug
Hello,
I want to call variants from RNA-seq data that I was provided in BAM format. I have already mark the duplicates, fixmate, fixed readgroups, fixed header information to work with the refseq format and sorted the reads. ValidateSamFile doesnt return any issues. This was able to solve all errors up until the current step: GATK4_MERGEVCFS.
I get the following error: java.lang.IllegalStateException: The elements of the input Iterators are not sorted according to the comparator htsjdk.variant.variantcontext.VariantContextComparator
The full error log:
nextflow.log
Command used and terminal output
nextflow run nf-core/rnavar -profile docker --input rnavar_test.csv --genome GRCh38 --skip_baserecalibration true --outdir rnavar -w /mnt/data/Till/work/Relevant files
No response
System information
Linux VM
(I run sarek on this same VM without problems)