The best way to get a consensus sequence based on the 1000genomes project official snp set it to use the vcf file and the vcftools
Our genotypes can be found in our release directories, we always distribute one file which contains all the sites and then one file per chr which contain the genotypes for all the individuals types
The data referred to in our recent paper is available from here
(See here for the paper http://www.1000genomes.org/announcem...mes-2012-10-31 which is freely available)
You can get a specific piece of one of our files using
You can generate a consensus using the vcftools perl script vcf-consensus
Please note
First this will reflect snps and indels but of course misses large copy number changes (I don't know if the script would handle our deletions)
Second the samtools mpileup version does work but it does not give you the consortium view on an individual but just the snps/indels predicted by samtools which is a different thing
Our genotypes can be found in our release directories, we always distribute one file which contains all the sites and then one file per chr which contain the genotypes for all the individuals types
The data referred to in our recent paper is available from here
(See here for the paper http://www.1000genomes.org/announcem...mes-2012-10-31 which is freely available)
You can get a specific piece of one of our files using
You can generate a consensus using the vcftools perl script vcf-consensus
Please note
First this will reflect snps and indels but of course misses large copy number changes (I don't know if the script would handle our deletions)
Second the samtools mpileup version does work but it does not give you the consortium view on an individual but just the snps/indels predicted by samtools which is a different thing
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