Question: Phastcons 46-Way Alignments To Annotate Variants That Fall Within Conserved Genomic Regions
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gravatar for ivivek_ngs
5.7 years ago by
ivivek_ngs4.8k
Seattle,WA, USA
ivivek_ngs4.8k wrote:

Dear All,

I am trying to annotate variants that fall within the conserved genomic regions with annovar script annotate_variation.pl. I have downloaded by the database in my /humandb folder of the annovar

path: /scratch/GT/vdas/tools/annovar/humandb/ -rwxrw-r-x 1 vdas DPT 115424594 Jan 30 2013 hg18_phastConsElements28way.txt -rwxrw-r-x 1 vdas DPT 205139082 Jan 30 2013 hg19_phastConsElements46way.txt

But when I am running the below script

perl /scratch/GT/vdas/tools/annovar/annotate_variation.pl --filter --buildver hg19 --dbtype mce46way /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/SNP_AD_annovar/T_S7999.recal_AD.snps.vcf.annovar /scratch/GT/vdas/tools/annovar/humandb/

I get the below error:

NOTICE: the --dbtype mce46way is assumed to be in generic ANNOVAR database format NOTICE: Variants matching filtering criteria are written to /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/SNP_AD_annovar/T_S7999.recal_AD.snps.vcf.annovar.hg19_mce46way_dropped, other variants are written to /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/SNP_AD_annovar/T_S7999.recal_AD.snps.vcf.annovar.hg19_mce46way_filtered NOTICE: Processing next batch with 27052 unique variants in 27052 input lines Error: cannot read from input database file /scratch/GT/vdas/tools/annovar/humandb/hg19_mce46way.txt: No such file or directory vdas@iit-n2:/scratch/GT/vdas/pietro/exome_seq/results/T_S7999/SNP_AD_annovar$

Even I tried to download it again using the below command: perl /scratch/GT/vdas/tools/annovar/annotate_variation.pl -downdb -webfrom annovar -buildver hg19 mce46way /scratch/GT/vdas/tools/annovar/humandb/

I get the below error: NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_phastConsElements46way.txt.gz ... Failed NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_phastConsElements46way.txt.idx.gz ... Failed WARNING: Some files cannot be downloaded, including http://www.openbioinformatics.org/annovar/download/hg19_phastConsElements46way.txt.idx.gz, http://www.openbioinformatics.org/annovar/download/hg19_phastConsElements46way.txt.gz

It seems the mce46way which is downloaded already in my cluster is not being recognized by annovar script as the name it is suggesting is different? Is there any other db file that I need to download to annotate my variants within conserved regions? I dont see any wrong command in the script. Did anyone face this issue? Please let me know where I am getting wrong. Any valuable suggestions are welcome.

Regards,

Vivek

annovar exome-sequencing snps • 2.7k views
ADD COMMENTlink written 5.7 years ago by ivivek_ngs4.8k
1

Why 46? UCSC just released 100 species conservation track.

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by PoGibas4.8k

How to retrieve it and then is the annovar compatible with this new track? Did anyone use this ? If so how do you change the command so that the annovar script recognizes the new 100 track conservation track

ADD REPLYlink written 5.7 years ago by ivivek_ngs4.8k

But I still dint receive the reply of the post I made. Did anyone face these kind of issues regarding the phastcons 46 database recognition? Please share

ADD REPLYlink written 5.7 years ago by ivivek_ngs4.8k
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