变异注释

老师,您好,我使用annovar注释变异的时候报错:Error: invalid record found in exonic_variant_function file (exonic format error): <line79synonymous SNVLOC119691921:XM_048633226.1#NC_063982.1#16995:exon3:c.C99T:p.L33L,LOC119691921:XM_048633233.1#NC_063982.1#16995:exon3:c.C99T:p.L33LNC_063982.11813318133CT0.43752219.779NC_063982.118133.CT2219.77PASSAC=7;AF=0.438;AN=16;BaseQRankSum=-2.632e+00;ClippingRankSum=0.00;DP=137;ExcessHet=0.1076;FS=3.160;MLEAC=7;MLEAF=0.438;MQ=60.00;MQRankSum=0.00;QD=29.60;ReadPosRankSum=0.296;SOR=0.283GT:AD:DP:GQ:PL0/0:16,0:16:48:0,48,5770/0:12,0:12:27:0,27,4050/0:13,0:13:39:0,39,5170/0:18,0:18:39:0,39,6080/1:9,12:21:99:317,0,3111/1:0,16:16:48:606,48,01/1:0,29:29:86:1027,86,01/1:0,9:9:27:332,27,0> at /mnt/data/home/tycloud/annovar/annovar/2019Oct24/coding_change.pl line 77, <EVF> line 1.

Error running system command: <coding_change.pl  /mnt/data/home/tycloud/my_reseq2/newvcf/snp.refGene.exonic_variant_function.orig /mnt/data/home/tycloud/my_reseq2/ref/unknown_refGene.txt /mnt/data/home/tycloud/my_reseq2/ref/unknown_refGeneMrna.fa -alltranscript -out /mnt/data/home/tycloud/my_reseq2/newvcf/snp.refGene.fa -newevf /mnt/data/home/tycloud/my_reseq2/newvcf/snp.refGene.exonic_variant_function>

Error running system command: </mnt/data/home/tycloud/annovar/annovar/2019Oct24/table_annovar.pl /mnt/data/home/tycloud/my_reseq2/newvcf/snp.avinput /mnt/data/home/tycloud/my_reseq2/ref -buildver unknown -outfile /mnt/data/home/tycloud/my_reseq2/newvcf/snp -remove -protocol refGene -operation g -nastring . -otherinfo>

是因为我从NCBI里下载的参考基因组格式有问题吗?参考基因组好像只有NCBI里有怎么办呢?这种情况下可以手动修改吗?

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1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

对的,NCBI上的参考基因组会有格式问题,需要手动调整才行;

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  • shidandan 提出于 2023-11-14 10:01

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