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WGLab / doc-ANNOVAR

Documentation for the ANNOVAR software
http://annovar.openbioinformatics.org
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annovar annotated, but no record in clinvar online #193

Open asmlgkj opened 2 years ago

asmlgkj commented 2 years ago

thanks a lot, professor wang. here is variant annotated by annovar, but no record in clinvar online . can you have a look? chr5 112162803 112162803 - G 799389 not_specified MedGen:CN169374 criteria_provided,_single_submitter Pathogenic NC_000005.9:g.112162808dup

kaichop commented 2 years ago

What is the command line that you used? Note that ANNOVAR always perform left normalization of variants. In the case of indels, it always use an annovar-specific format that use '-' to denote null nucleotide.

On Sat, May 21, 2022 at 5:47 AM curry_fan @.***> wrote:

thanks a lot, professor wang. here is variant annotated by annovar, but no record in clinvar online . can you have a look? chr5 112162803 112162803 - G 799389 not_specified MedGen:CN169374 criteria_provided,_single_submitter Pathogenic NC_000005.9:g.112162808dup

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asmlgkj commented 2 years ago

thanks a lot. here is my command. table_annovar.pl my.vcf /annovar/humandb -buildver hg19 -out my.anno -remove -protocol refGeneWithVer,1000g2015aug_all,clinvar_20211002,avsnp150,cosmic94,dbnsfp41c -operation g,f,f,f,f,f -argument '-hgvs,-hgvs,-hgvs,-hgvs,-hgvs,-hgvs' -nastring . -vcfinput -polish

asmlgkj commented 2 years ago

in the vcf, it is a record as follows

chr5 112162803 . A AG

asmlgkj commented 2 years ago

is there any comments about this? thanks a lot