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.
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