Question: Does anyone knows how to generate dbSNP "Reference-Ordered Data" (ROD) file ?
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3.1 years ago by
United States
bio_vitus0 wrote:

I like to know how to generate dbSNP "Reference-Ordered Data" (ROD) file from dbSNP data and is it possible

to generate it for per human chromosomes.

Appreciate your help.




dbsnp • 1.2k views
ADD COMMENTlink modified 3.1 years ago by Jennifer Hillman Jackson25k • written 3.1 years ago by bio_vitus0
gravatar for Jennifer Hillman Jackson
3.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


ROD data is reference annotation that is anchored by genomic position. This makes it easy to compare two datasets together using position.

If you use the built-in human hg_g1k_v37 genome (1000 genomes), then dbSNP is already indexed (sourced from the GATK resource bundle). If you want to use hg38/hg19 or any other build, then the idea is to locate a VCF dataset based on the same exact reference data (dbSNP or any other annotation that you want to link in). GATK itself, NCBI, UCSC, and others can be good data sources. A google should help narrow down the choices.

This prior Biostars question addresses essentially the same question with the bonus of covering the importance of confirming format (including the ordering of chromosomes in input data). Hopefully it will help:

This might help as well, when deciding on which genome to use (hg_g1k_v37 or another as a Custom genome). It covers the details of that genome, plus format, and chromosome order when using a CG or linking in other annotaion data: Fasta Format, Custom Genomes, and GATK Chromosome ordering

If you just want to work on one chromosome, then you can use the full ROD dataset but only include the VCF containing the variant calls for the chromosome of interest. Or you can filter both down. Use the tool VCF Filter.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Jennifer Hillman Jackson25k
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