![]() How do I find the most up-to-date data?. ![]() As methods were developed during the 1000 Genomes Project, it is recommended to use the final phase 3 data in preference to earlier call sets. This was the approach used in phase 1 of the 1000 Genomes Project. Depth of coverage, base quality and mapping quality were also used when making this decision. In most cases, the highest frequency alternative allele was chosen and genotyped. In earlier phases of the 1000 Genomes Project, the programs used for genotyping were unable to genotype sites with more than two alleles. ![]() The supplementary information for both papers provides further detail. More information can be found in the main phase 3 publication from the 1000 Genomes Project and the structural variation publication. While bi-allelic calling was used in earlier phases of the 1000 Genomes Project, multi-allelic SNPs, indels, and a diverse set of structural variants (SVs) were called in the final phase 3 call set. Are all the genotype calls in the 1000 Genomes Project VCF files bi-allelic? Our VCFs are multi-individual, with genotypes listed for each sample we do not have individual or population specific VCFs. As these have been released at different times, they are on different versions of the format - this will be indicated in the file heading.
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