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Hi,
in our pipeline, I'd like to annotate the resulting vcf files with 1000 Genome phase 1 allele frequencies. I cannot use Annovar, because part of our sequencing results are used for diagnostic purposes, which means commercial use.
My idea is to download all vcf files from 1000 Genomes, concatenate them and then use SnpSift (something like: ./SnpSift annotate combined_1000G.vcf input.vcf > output.vcf -noId -info 1000Gp1_AF)
I wonder if someone has a better solution, e. g. not requiring such an enormous dataset download.
The dbNSFP option of SnpSift is not sufficient, because I also need the frequencies of the synonymous SNVs.
in our pipeline, I'd like to annotate the resulting vcf files with 1000 Genome phase 1 allele frequencies. I cannot use Annovar, because part of our sequencing results are used for diagnostic purposes, which means commercial use.
My idea is to download all vcf files from 1000 Genomes, concatenate them and then use SnpSift (something like: ./SnpSift annotate combined_1000G.vcf input.vcf > output.vcf -noId -info 1000Gp1_AF)
I wonder if someone has a better solution, e. g. not requiring such an enormous dataset download.
The dbNSFP option of SnpSift is not sufficient, because I also need the frequencies of the synonymous SNVs.