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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

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