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Effect annotated whole genome variants for 163 vervet monkeys (SNPs, Indels, and macaque fixed differences)

ABSTRACT: Callset of filtered SNP and indel genotypes of 163 vervet monkeys (genus Chlorocebus) from several African and Caribbean countries as described in Svardal et al. Nature Genetics 2017. Sample information can be found in Data S1 of the publication above. There is one VCF file per chromosome. Genotypes are not imputed and unphased. There is missing data. Note that there also is a imputed and phased dataset of biallelic SNPs available as a separate submission which might be more useful for many applications. Fixed differences between vervet and macaque have been added to the VCFs (mainly the sites with AC=0 and AF=0.000) so that variant effects are also annotated for divergent sites between vervet and macaque. Where available, the macaque state is given by the INFO tag 'AA'. Variant effects have been annotated. Please refer to the methods section of the article cited above for a full description of the data. <hannes.svardal@gmail.com>

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Chlorocebus Sabaeus

SUBMITTER: Gregor Mendel Institute

PROVIDER: PRJEB22989 | EVA | 2017-11-06

REPOSITORIES: EVA

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			Action	DRS
	Svardal_et_al_2017_vervet_monkey_SNPs_incl_rhesus_macaque_diff_SnpEff_ensembl_1.1.78_CAE12.vcf.gz	Vcf
	Svardal_et_al_2017_vervet_monkey_SNPs_incl_rhesus_macaque_diff_SnpEff_ensembl_1.1.78_CAE12.vcf.gz.md5	Vcf
	Svardal_et_al_2017_vervet_monkey_SNPs_incl_rhesus_macaque_diff_SnpEff_ensembl_1.1.78_CAE12.vcf.gz.tbi	Vcf
	Svardal_et_al_2017_vervet_monkey_SNPs_incl_rhesus_macaque_diff_SnpEff_ensembl_1.1.78_CAE12.vcf.gz.tbi.md5	Vcf
	Svardal_et_al_2017_vervet_monkey_SNPs_incl_rhesus_macaque_diff_SnpEff_ensembl_1.1.78_CAE22.vcf.gz	Vcf

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