For general definitions of these terms, see this Dictionary entry.
If you're working with human data, you're in luck. We provide all resource files necessary for applying the Best Practices pipelines to human data as part of our Resource Bundle, and we provide specific recommendations on which sets to use for each tool in the variant calling pipelines, as well as default settings for all parameters. See the Best Practices documentation for details to that effect.
Unfortunately we're not currently able to provide centralized resources for non-human organisms. That means you will need to do some additional homework to find out what is available for your organism. In order to facilitate this process, we have created a forum topic called "Non-Human" specifically for the purpose of collecting information on this topic. We invite researchers who have experience in non-human genomics analysis to share their knowledge by contributing documentation to this section.
I have some doubts and I hope anyone could help me.
I'm trying to run gatk pipeline again (I did before successfully), and I decided to use as known site, dbSNP last release (v153).
So, I've downloaded this dataset: GCF_000001405.25.gz (and .tbi also), from dbSNP FTP which is a vcf file from dbSNP v153, using GRCh37 as reference.
As other know sites, I will use Mills and 1000g vcf's available at FTP bundle from Broad Inst.
I noticed that dbSNP vcf have chrom names like "NC_...", "NT_...". But other vcf's from bundle are named as "chr1", "chr2"... accordingly to UCSC hg19 reference.
So, my questions are:
1) Is it recommended simply change chrom names to equivalent ones? Is this correct and recommended, without major problems? Example:
Change "NC_000001.10" to "chr1"
Change "NC_000002.11" to "chr2"
Change "NC_000003.11" to "chr3"
Change "NC_012920.1" to "chrM"
2) What do you think about: download dbSNP v153 in GRCh38 version in order to make the liftover to hg19 (using chain table file from UCSC -- with chrom names from UCSC)? Is this ok?
3) If none of the above, do you have any advice for me, to deal with it?
Further, I couldn't find any other website/ftp which I could download dbSNP v153 with UCSC hg19 chrom names.
I'm trying to find a solution. Hope you could help me.
Thank you for your time and patience.
The "Resource Bundle" link is broken...
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