table_annovar.pl ./ -buildver all_sample_INS_DEL.vcf.gz -out all_sample_INS_DEL -remove -protocol refGene -operation g -nastring . -vcfinput
##报错如下，all_sample_INS_DEL.vcf.gz和unknow相关文件见附件
NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)
NOTICE: Running with system command <convert2annovar.pl -includeinfo -allsample -withfreq -format vcf4 all_sample_INS_DEL.vcf.gz > all_sample_INS_DEL.avinput>
NOTICE: Finished reading 6401 lines from VCF file
NOTICE: A total of 6371 locus in VCF file passed QC threshold, representing 0 SNPs (0 transitions and 0 transversions) and 6371 indels/substitutions
NOTICE: Finished writing allele frequencies based on 0 SNP genotypes (0 transitions and 0 transversions) and 6371 indels/substitutions for 0 samples
NOTICE: Running with system command </home/lx_sky6/software/annovar/table_annovar.pl all_sample_INS_DEL.avinput ./ -buildver unknown -outfile all_sample_INS_DEL -remove -protocol refGene -operation g -nastring . -otherinfo>
NOTICE: the --polish argument is set ON automatically (use --nopolish to change this behavior)
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NOTICE: Processing operation=g protocol=refGene
NOTICE: Running with system command <annotate_variation.pl -geneanno -buildver unknown -dbtype refGene -outfile all_sample_INS_DEL.refGene -exonsort -nofirstcodondel all_sample_INS_DEL.avinput ./>
NOTICE: Output files are written to all_sample_INS_DEL.refGene.variant_function, all_sample_INS_DEL.refGene.exonic_variant_function
NOTICE: Reading gene annotation from ./unknown_refGene.txt ... Done with 43480 transcripts (including 0 without coding sequence annotation) for 43480 unique genes
NOTICE: Processing next batch with 6371 unique variants in 6371 input lines
NOTICE: Reading FASTA sequences from ./unknown_refGeneMrna.fa ... Done with 267 sequences
NOTICE: Running with system command <coding_change.pl all_sample_INS_DEL.refGene.exonic_variant_function.orig .//unknown_refGene.txt .//unknown_refGeneMrna.fa -alltranscript -out all_sample_INS_DEL.refGene.fa -newevf all_sample_INS_DEL.refGene.exonic_variant_function>
Error: invalid notation found: <Rla1A25863:Rla1A25863-mRNA-1:exon3:c.578_579insTGGATCTTATGGGCAAGGACCGAGTGGTGGATCTTATGGGCAAGGACCGAGTGG:p.D193delinsDGSYGQGPSGGSYGQGPSG> at /home/lx_sky6/software/annovar/coding_change.pl line 617, <EVF> line 1.
Error running system command: <coding_change.pl all_sample_INS_DEL.refGene.exonic_variant_function.orig .//unknown_refGene.txt .//unknown_refGeneMrna.fa -alltranscript -out all_sample_INS_DEL.refGene.fa -newevf all_sample_INS_DEL.refGene.exonic_variant_function>
Error running system command: </home/lx_sky6/software/annovar/table_annovar.pl all_sample_INS_DEL.avinput ./ -buildver unknown -outfile all_sample_INS_DEL -remove -protocol refGene -operation g -nastring . -otherinfo>