All new development is being done against Grch38/hg38. Note that many of these resources are out of date and will eventually be retired. The Broad's custom exome targets list: 37.interval_list (note that you should always use the exome targets list that is appropriate for your data, which typically depends on the prep kit that was used, and should be available from the kit manufacturer's website).Īdditionally, these files all have supplementary indices, statistics, and other QC data available.Note that this resource is out of date and does not represent the results of our Best Practices. A callset produced by running UnifiedGenotyper on the dataset above..37.20.bam containing ~64x reads of NA12878 on chromosome 20.A large-scale standard single sample BAM file for testing:.The latest set from 1000G phase 3 (v4) for genotype refinement: 1000G_phase3_v4_.1000G_ (currently from the 1000 Genomes Phase I indel calls).The current best set of known indels to be used for local realignment (note that we don't use dbSNP for this anymore) use both files:.OMNI 2.5 genotypes for 1000 Genomes samples, as well as sites, VCF.The same file subsetted to only sites discovered in or before dbSNPBuildID 129, which excludes the impact of the 1000 Genomes project and is useful for evaluation of dbSNP rate and Ti/Tv values at novel sites.
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