Comments (6)
$ tail $Sample.refGeneWithVer.fa
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Hi Kaichop
I annotate the "chr22 39381817 39381817 - CAA" variant, It's ok.
Then I split avinput by chromosome, and annotate separately by Annovar. At last I confirm this error happend on chrX chromosome, but still can't determine which position variant.
I upload my chrX avinput file, temporary file and logs.
$ /work/Software/annovar_2018-04-16/table_annovar.pl ../chrX.avinput $Anno_db -buildver hg38 -out chrX --checkfile --otherinfo -polish -protocol cytoBand,refGeneWithVer,ensGene,knownGene -operation r,g,g,g -nastring -
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I found "chrX 1403271 1403271 A - " variant will cause this error.
My hg38_refGeneWithVer.txt info contain this position:
hg38_refGeneWithVer.xlsx
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Thanks kaichop,
I have found the reason. When I build hg38_refGeneMrna.fa from hg38_refGene.txt, I choose hg38 refgenome fasta file from GATK bundle database. But this file mask some region of chromosome with 'N'. So I got the error hg38_refGeneMrna.fa.
Then, I rebuild hg38_refGeneMrna.fa, and choose refgenome fasta from UCSC. I solved this problem.
Thanks again!
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Related Issues (20)
- Invalid record HOT 3
- Multiple errors for hg38? HOT 2
- I found some bugs in the refGene.txt HOT 2
- Error: the required database file annovar/AT_refGeneMrna.txt/hg18_refGene.txt does not exist. HOT 3
- Cannot able to download annotations from annovar HOT 4
- Indels are removing as invalid input HOT 3
- wAnnovar down? HOT 2
- wannovar.wglab.org down? HOT 1
- Annovar not responding
- revel format ? HOT 7
- annotate.variation.pl showing error
- zygosity column
- Index file for gnomad database from gnomad website
- Database Downloads Failing HOT 1
- Downloading annotation database ....Failed HOT 4
- multianno.txt to multianno.vcf HOT 1
- Annotation of double base substitutions (DBS,DNP) HOT 5
- prepare_annovar_user.pl not working with COSMIC version 99 HOT 2
- Download hg38 Gnomad DB HOT 1
- Truncated VCF output at chr21 HOT 2
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