Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

evaluate SNPcalling

sepandsepand BarcelonaMember

I did SNP calling with samtools mpileup and now I want to produce some stats about my SNPs to make filtering. my samples are from a great tit (Parus major). I tried to used VariantEval tool but for VariantEval it seems that we need dbSNP file from the reference genome.
I found these file in the dbSNP database for parus major but the files seems empty
ftp://ftp.ncbi.nih.gov/snp/organisms/pmajor_9157/VCF/
the whole genome of this species is available but I want to know how to download dbSNPs file ? https://www.ncbi.nlm.nih.gov/projects/SNP/snp_retrieve.cgi?subsnp_id=161110036
here it seems there is no information about the assembly .
here is the link for genome data :https://www.ncbi.nlm.nih.gov/genome/?term=parus+major

Thanks a lot,
Sepand

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited February 2017

    @sepand
    Hi Sepand,

    Sorry for the late response. I am a little confused by your question. I just went to the sites you linked to, and I am able to download the VCFs with the known variation in your sample.

    -Sheila

Sign In or Register to comment.