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>
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