Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences

Question

[sainavyav22]

Hello,

I am using ANNOVAR to perform variant annotation of my dog tumor reads. I am facing issues to generate the annotation data base. I have used the following protocol.

1. I have downloaded the dog genome annotation file in GFF format from NCBI database, then converted it into genePred file to generate dog_refGene.txt file.

2. I ran the following commands, that are provided in the annovar website to generate annotation database for other than human genome.

   perl annotate_variation.pl --buildver CanFam3.1 --downdb seq dogdb/CanFam3.1_seq -fastafile GCF_000002285.3_CanFam3.1_genomic.fna perl retrieve_seq_from_fasta.pl dogdb/CanFam3.1_refGene.txt -seqdir dogdb/CanFam3.1_seq -format refGene -outfile dogdb/CanFam3.1_refGeneMrna.fa -fastafile GCF_000002285.3_CanFam3.1_genomic.fna

There it is mentioned to run the both commands consequently. After running the first command I received the following warning message, and the second command is not running.

*NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/chromFa.zip ... Failed
NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/chromFa.tar.gz ... Failed
NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/CanFam3.1.chromFa.tar.gz ... Failed
NOTICE: Downloading annotation database http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/CanFam3.1.fa.gz ... Failed
WARNING: Some files cannot be downloaded, including http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/chromFa.tar.gz, http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/CanFam3.1.fa.gz, http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/chromFa.zip, http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/CanFam3.1.chromFa.tar.gz*

Can someone please help with this. How to generate the annotation database for genome to use in ANNOVAR or Is there any other annotation platforms for better annotation? Thanks.

[Pierre Lindenbaum]

the URL is

https://hgdownload.soe.ucsc.edu/goldenPath/canFam3/bigZips/

not

http://hgdownload.cse.ucsc.edu/goldenPath/CanFam3.1/bigZips/

you should look in those perl script where the URL to the UCSC is constructed

[sainavyav22]

Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks for helping.