Hi,
I recently discovered your tool and I am using mutserve (v2.0.3) to detect variants in the mouse mitogenome. I am using the following command-line:
mutserve call --reference {mtFasta} --contig-name MT --output {vcfFile} {bamFile}The tool seems to partially work, as it generates a {sampleName}_mutserve.txt file which lists detected variants in a tabular format. But before it can produce the output vcf file it stops with the following error:
✔️ Merge output files
htsjdk.samtools.SAMException: Sequence name 'MT dna:chromosome chromosome:GRCm39:MT:1:16299:1 REF' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'
at htsjdk.samtools.SAMSequenceRecord.validateSequenceName(SAMSequenceRecord.java:336)
Is there a solution for this? Thank you for dealing with my question.
Hi,
I recently discovered your tool and I am using mutserve (v2.0.3) to detect variants in the mouse mitogenome. I am using the following command-line:
mutserve call --reference {mtFasta} --contig-name MT --output {vcfFile} {bamFile}The tool seems to partially work, as it generates a {sampleName}_mutserve.txt file which lists detected variants in a tabular format. But before it can produce the output vcf file it stops with the following error:
Is there a solution for this? Thank you for dealing with my question.