Extracting Individual Allele Frequencies From A Vcf File
Hi all, I have used SAMtools to identify SNPs within 3 separate individuals and have generated a VCF file. I am able to extract the depth for each individual but am struggling to get the allele frequency at each SNP for each individual. The VCF contains an overall alternative allele frequency but I would like this broken down per individual. If anybody knows if this is possible and how to do it I'd be grateful for any advice. Thanks!
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Maxime Lamontagne
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Jitendra •
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Jitendra •
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I think this should work. You need vcftools to do this.
The first command will isolate the genotype for Subject1:
.../tabix-0.2.3/vcftools_0.1.4a/perl/vcf-subset -c Subject1 genotypes.vcf > temp.vcf
The second one will transform the data in frequency:
.../tabix-0.2.3/vcftools_0.1.4a/cpp/vcftools --vcf temp.vcf --freq --out Subject1.SNP.allelefrequencies
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Just a couple quick questions to clarify: Does each individual have their own VCF file? Are you looking for the allele frequency for each SNP in the general population -- or in each individual? Generally the last columns in the VCF (the ones that start [1/1] or [0/1] etc) are the allele frequencies in the individual for that variant. Maybe to clarify even more you could post a couple lines from your VCF.
Using this command "vcftools --vcf aln.vcf --freq" I have got only 3 types of allele frequencies: 0, 0.5 and 1. Could somebody advice me how to get real frequencies at certain posiitions? Thanks a lot.
Yes, you will get 3 frequencies only, either homozygous SNPs (0 and 1) and heterozygous SNPs (0.5 and 0.5)
I have extracted the following members of variants.
'AC', 'AF', 'ALT', 'AN', 'ANN', 'AO', 'ASP', 'ASS', 'CAF', 'CDA', 'CFL', 'CHROM', 'COMMON', 'DP', 'DSS', 'FAO', 'FDP', 'FILTER_NOCALL', 'FILTER_PASS', 'FR', 'FRO', 'FSAF', 'FSAR', 'FSRF', 'FSRR', 'FWDB', 'FXX', 'G5', 'G5A', 'GENEINFO', 'GNO', 'HD', 'HRUN', 'HS', 'ID', 'INT', 'KGPROD', 'KGPhase1', 'KGPilot123', 'KGValidated', 'LEN', 'LOF', 'LSD', 'MLLD', 'MTP', 'MUT', 'NMD', 'NOC', 'NOV', 'NS', 'NSF', 'NSM', 'NSN', 'OALT', 'OID', 'OM', 'OMAPALT', 'OPOS', 'OREF', 'OTH', 'OTHERKG', 'PB', 'PBP', 'PH3', 'PM', 'PMC', 'POS', 'QD', 'QUAL', 'R3', 'R5', 'RBI', 'REF', 'REFB', 'REVB', 'RO', 'RS', 'RSPOS', 'RV', 'S3D', 'SAF', 'SAO', 'SAR', 'SF', 'SLO', 'SRF', 'SRR', 'SSEN', 'SSEP', 'SSR', 'SSSB', 'STB', 'STBP', 'SYN', 'TPA', 'TYPE', 'U3', 'U5', 'VARB', 'VC', 'VLD', 'VP', 'WGT', 'WTD', 'altlen', 'dbNSFP_SIFT_score', 'dbSNPBuildID', 'is_snp', 'numalt' Which attributes usually determine SNP?