以下是我做位点注释的annotated_variants.refGene.exonic_variant_function.orig文件内容：line3523389 nonsynonymous SNV Os10g0100200:Os10t0100200-01:exon1:c.G87C:p.W29C chr10 44989 44989 G C . . .，但是总是报错：NOTICE: Running with system command <coding_change.pl /work/my_reseq/innovation.refGene.exonic_variant_function.orig /work/my_reseq/ref/unknown_refGene.txt /work/my_reseq/ref/unknown_refGeneMrna.fa -alltranscript -out /work/my_reseq/innovation.refGene.fa -newevf /work/my_reseq/innovation.refGene.exonic_variant_function>
Error: invalid record found in exonic_variant_function file (exonic format error): <line3523389 nonsynonymous SNV Os10g0100200:Os10t0100200-01:exon1:c.G87C:p.W29C chr10 44989 44989 G C . . . chr10 44989 vg1000044989 G C . . .> at /share/work/biosoft/annovar/latest/coding_change.pl line 77, <EVF> line 1.
Error running system command: <coding_change.pl /work/my_reseq/innovation.refGene.exonic_variant_function.orig /work/my_reseq/ref/unknown_refGene.txt /work/my_reseq/ref/unknown_refGeneMrna.fa -alltranscript -out /work/my_reseq/innovation.refGene.fa -newevf /work/my_reseq/innovation.refGene.exonic_variant_function>
Error running system command: </share/work/biosoft/annovar/latest/table_annovar.pl /work/my_reseq/innovation.avinput /work/my_reseq/ref -buildver unknown -outfile /work/my_reseq/innovation -remove -protocol refGene -operation g -nastring . -otherinfo>（请问老师这是为什么？哪里出错了？怎么一直出错啊，我应该怎么跑啊？）
annotated_variants.refGene.exonic_variant_function.orig文件内容：line3523389 nonsynonymous SNV Os10g0100200:Os10t0100200-01:exon1:c.G87C:p.W29C chr10 44989 44989 G C . . . chr10 44989 vg1000044989 G C . . .
line3523409 nonsynonymous SNV Os10g0100300:Os10t0100300-01:exon10:c.T1419G:p.S473R chr10 46376 46376 A C . . . chr10 46376 vg1000046376 A C . .
line3523410 nonsynonymous SNV Os10g0100300:Os10t0100300-01:exon10:c.T1310C:p.V437A chr10 46485 46485 A G . . . chr10 46485 vg1000046485 A G . .
avinput文件内容：
chr0112031203TC...chr011203vg0100001203TC...
chr0112491249AC...chr011249vg0100001249AC...
chr0112661266GA...chr011266vg0100001266GA...
chr0112771277TC...chr011277vg0100001277TC...
chr0113251325CT...chr011325vg0100001325CT...
innovation.refGene.variant_function文件内容：
intergenicNONE(dist=NONE),NONE(dist=NONE)chr0112031203TC...chr011203vg0100001203TC...
intergenicNONE(dist=NONE),NONE(dist=NONE)chr0112491249AC...chr011249vg0100001249AC...
intergenicNONE(dist=NONE),NONE(dist=NONE)chr0112661266GA...chr011266vg0100001266GA...
intergenicNONE(dist=NONE),NONE(dist=NONE)chr0112771277TC...chr011277vg0100001277TC...
intergenicNONE(dist=NONE),NONE(dist=NONE)chr0113251325CT...chr011325vg0100001325CT...
intergenicNONE(dist=NONE),NONE(dist=NONE)chr0113351335GT...chr011335vg0100001335GT...
运行代码如下：
table_annovar.pl $workdir/innovation/cleaned_for_annovar.vcf $refdir \
-buildver unknown -out $workdir/innovation
-remove -protocol refGene -operation g -nastring . -vcfinput