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Hello Prof. Wang
Thanks for developing ANNOVAR! I am experiencing a small use after successfully performing a gene-based annotation for a number of GWAS variants:
I am using dbSNP151 on the hg38…
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When initally running gemBS extract, I do not see any variants in the _snps.txt.gz files. The he _snps.txt.gz file is empty.
I execute the following commands to extract wgbs samples SNPs info:
`ge…
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I am trying to run SAIGE-GWAS Gene and Region Based Association Tests, and I am trying to figure out how to obtain legitimate groupfiles to use for the analysis. I know there is an R-script available,…
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Hi,
First, thanks for all the hard work.
When I try to download the InterVar database using:
./annotate_variation.pl -build hg19 -downdb intervar_20180118 humandb/
the screen output is (no…
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Hello,
I have generated the annotations based on annovar and found that indels are not getting annotated and are getting removed from the dataset. Is there a way to work around it?
Regards
Akhi…
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I found that DBS are not annotated correctly. For example:
12 115109872 115109873 GG AA (Hg19)
annotated as "nonframeshift substitution" while the main outcome is nonsynonymous mutation in TBX3 …
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The install.sh script checks for genome file /vlsci/VR0193/shared/cpipe/hg19/hg19.genome and tries to download it if it doesn't exist. This automatic download is only possible on machines with mysql (…
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Dear Prof. Wang,
I'm sorry for interrupting you.
I am using ANNOVAR to annotate my vcf file. When I used convert2annovar.pl to convert vcf file into an avinput file, I found a problem. All my vari…
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I have the most previous experience with SnpEff/ClinEff. Do people here have preferences as to which tool if any to run and any non-standard parameters to use?
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we have been annotated the vcf, and then we run "python /opt/Intervar.py -b hg19 -i /opt/annovar.hg19_multianno.vcf --input_type=VCF -o out.vcf " there show error and dose't work.
I really need to k…