Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error: invalid record found in exonic_variant_function file (exonic format error) #216

Open
AnujaM1611 opened this issue Mar 21, 2023 · 0 comments

Comments

@AnujaM1611
Copy link

Dear professor Kai:

I am working with mycobacterium tuberculosis genome (H37Rv). I have downloaded GFF3 from NCBI and converted to gtf (using gffread). Refgene db was built as given here : https://annovar.openbioinformatics.org/en/latest/user-guide/gene/#what-about-gff3-file-for-new-species.

While running table_annovar.pl, I am getting error: invalid record found in exonic_variant_function file.
Below are all details:

command: perl table_annovar.pl P14.hard-filtered.vcf . -buildver AT -out EXAMPLE2 -remove -protocol refGene -operation g -nastring . -vcfinput

Files : Refgene.txt is attached for reference.

Complete error: Error: invalid record found in exonic_variant_function file (exonic format error): <line1 nonsynonymous SNV :gene-Rv0005:exon1:c.G873C:p.M291I NC_000962.3 6112 6112 G C 144.36 3 NC_000962.3 6112 . G C 44.36 PASS AC=2;AF=1.000;AN=2;DP=3;FS=0.000;MQ=250.00;MQRankSum=0.000;QD=14.79;ReadPosRankSum=0.000;SOR=2.833;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/1:0,3:1.000:3:0,3:0,0:7:81,9,0:4.4361e+01,6.6312e+00,1.0638e+00:0.00,34.77,37.77:0,0,3,0:0,0,3,0> at ./coding_change.pl line 77, line 1.
Error running system command: <coding_change.pl EXAMPLE2.refGene.exonic_variant_function.orig ./AT_refGene.txt ./AT_refGeneMrna.fa -alltranscript -out EXAMPLE2.refGene.fa -newevf EXAMPLE2.refGene.exonic_variant_function>
Error running system command: <table_annovar.pl EXAMPLE2.avinput . -buildver AT -outfile EXAMPLE2 -remove -protocol refGene -operation g -nastring . -otherinfo>

Can you please help me with this?

Thanks in advance.
AT_refGene.txt

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant