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Dear authors, I am trying to run svict with a gtf file to annotate variants.
I downloaded the gtf from igenomes and I get an error message of wrong file format.
I also tried to add an header to the gtf but this did not fix the issue.
Could you please help? code below
aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/ ./references/Homo_sapiens/UCSC/hg19/Annotation/Genes/ --exclude "*" --include "genes.gtf"
svict -P -i myfile.bam -r ./ucsc.hg19.fasta -g ./references/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf
-o myfile.annot
Error: Specified GTF file (references/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf) does not appear to be correctly formatted, or is missing a header.
The text was updated successfully, but these errors were encountered:
Dear authors, I am trying to run svict with a gtf file to annotate variants.
I downloaded the gtf from igenomes and I get an error message of wrong file format.
I also tried to add an header to the gtf but this did not fix the issue.
Could you please help? code below
The text was updated successfully, but these errors were encountered: