VCF summary information
Example VCF file
We need an example VCF file for demonstation. You can manually download it from link (877KB) and put the file in your current working directory. Or, within Julia,
isfile("test.08Jun17.d8b.vcf.gz") || download("http://faculty.washington.edu/browning/beagle/test.08Jun17.d8b.vcf.gz", joinpath(pwd(), "test.08Jun17.d8b.vcf.gz")) stat("test.08Jun17.d8b.vcf.gz")
StatStruct(mode=0o100644, size=876514)
The first 35 lines of the VCF file are
using VCFTools fh = openvcf("test.08Jun17.d8b.vcf.gz", "r") for l in 1:35 println(readline(fh)) end close(fh)
##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD"> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder"> ##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder"> ##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder"> ##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder"> ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants"> ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants"> ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record"> ##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints"> ##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints"> ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles"> ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> ##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count"> ##ALT=<ID=DEL,Description="Deletion"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder"> ##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods"> ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele, ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/technical/reference/ancestral_alignments/README"> ##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN"> ##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN"> ##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN"> ##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN"> ##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN"> ##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents"> ##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data"> ##reference=GRCh37 ##reference=GRCh37 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100 HG00101 HG00102 HG00103 HG00104 HG00106 HG00108 HG00109 HG00110 HG00111 HG00112 HG00113 HG00114 HG00116 HG00117 HG00118 HG00119 HG00120 HG00121 HG00122 HG00123 HG00124 HG00125 HG00126 HG00127 HG00128 HG00129 HG00130 HG00131 HG00133 HG00134 HG00135 HG00136 HG00137 HG00138 HG00139 HG00140 HG00141 HG00142 HG00143 HG00146 HG00148 HG00149 HG00150 HG00151 HG00152 HG00154 HG00155 HG00156 HG00158 HG00159 HG00160 HG00171 HG00173 HG00174 HG00176 HG00177 HG00178 HG00179 HG00180 HG00182 HG00183 HG00185 HG00186 HG00187 HG00188 HG00189 HG00190 HG00231 HG00232 HG00233 HG00234 HG00235 HG00236 HG00237 HG00238 HG00239 HG00240 HG00242 HG00243 HG00244 HG00245 HG00246 HG00247 HG00249 HG00250 HG00251 HG00252 HG00253 HG00254 HG00255 HG00256 HG00257 HG00258 HG00259 HG00260 HG00261 HG00262 HG00263 HG00264 HG00265 HG00266 HG00267 HG00268 HG00269 HG00270 HG00271 HG00272 HG00273 HG00274 HG00275 HG00276 HG00277 HG00278 HG00280 HG00281 HG00282 HG00284 HG00285 HG00306 HG00309 HG00310 HG00311 HG00312 HG00313 HG00315 HG00318 HG00319 HG00320 HG00321 HG00323 HG00324 HG00325 HG00326 HG00327 HG00328 HG00329 HG00330 HG00331 HG00332 HG00334 HG00335 HG00336 HG00337 HG00338 HG00339 HG00341 HG00342 HG00343 HG00344 HG00345 HG00346 HG00349 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As in typical VCF files, it has a bunch of meta-information lines, one header line, and then one line for each each marker. In this VCF, genetic data has fields GT (genotype), DS (dosage), and GL (genotype likelihood).
Summary statistics
- Number of records (markers) in a VCF file.
records = nrecords("test.08Jun17.d8b.vcf.gz")
1356
- Number of samples (individuals) in a VCF file.
samples = nsamples("test.08Jun17.d8b.vcf.gz")
191
gtstatsfunction calculates genotype statistics for each marker with GT field.
@time records, samples, lines, missings_by_sample, missings_by_record, maf_by_record, minorallele_by_record = gtstats("test.08Jun17.d8b.vcf.gz");
0.914261 seconds (2.04 M allocations: 197.348 MiB, 3.84% gc time)
# number of markers records
1356
# number of samples (individuals) samples
191
# number of markers with GT field lines
1356
# number of missing genotypes in each sample (individual) missings_by_sample'
1×191 RowVector{Int64,Array{Int64,1}}:
0 0 0 0 0 0 0 0 0 0 0 0 0 … 0 0 0 0 0 0 0 0 0 0 0 0
# number of missing genotypes in each marker with GT field missings_by_record'
1×1356 RowVector{Int64,Array{Int64,1}}:
0 0 0 0 0 0 0 0 0 0 0 0 0 … 0 0 0 0 0 0 0 0 0 0 0 0
# minor allele frequency of each marker with GT field maf_by_record'
1×1356 RowVector{Float64,Array{Float64,1}}:
0.0 0.0 0.0 0.0 0.146597 0.0 … 0.0 0.0 0.0706806 0.0706806 0.0
# minor allele of each marker (with GT field): true (REF) or false (ALT) minorallele_by_record'
1×1356 RowVector{Bool,Array{Bool,1}}:
true true true true true true … true true true true true true
The optional second argument of gtstats function specifies an output file or IO stream for genotype statistics per marker. Each line has fields:
- 1-8: VCF fixed fields (CHROM, POS, ID, REF, ALT, QUAL, FILT, INFO)
- 9: Missing genotype count
- 10: Missing genotype frequency
- 11: ALT allele count
- 12: ALT allele frequency
- 13: Minor allele count (REF allele vs ALT alleles)
- 14: Minor allele frequency (REF allele vs ALT alleles)
- 15: HWE P-value (REF allele vs ALT alleles)
# write genotype statistics in file gtstats.out.txt @time gtstats("test.08Jun17.d8b.vcf.gz", "gtstats.out.txt");
0.207211 seconds (1.37 M allocations: 159.816 MiB, 10.48% gc time)
The output file can be read as a DataFrame for further analysis.
using DataFrames gstat = readtable("gtstats.out.txt"; header = false, separator = '\t', names = [:chr, :pos, :id, :ref, :alt, :qual, :filt, :info, :missings, :missfreq, :nalt, :altfreq, :nminor, :maf, :hwe], eltypes = [String, Int, String, String, String, String, String, String, Int, Float64, Int, Float64, Int, Float64, Float64] )
| chr | pos | id | ref | alt | qual | filt | info | missings | missfreq | nalt | altfreq | nminor | maf | hwe | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 22 | 20000086 | rs138720731 | T | C | 100 | PASS | AC=7;RSQ=0.8454;AVGPOST=0.9983;AA=T;AN=2184;LDAF=0.0040;THETA=0.0001;VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0003;AF=0.0032;AFR_AF=0.01 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 2 | 22 | 20000146 | rs73387790 | G | A | 100 | PASS | LDAF=0.0169;RSQ=0.9482;THETA=0.0004;AA=G;AN=2184;AVGPOST=0.9972;VT=SNP;SNPSOURCE=LOWCOV;AC=36;ERATE=0.0003;AF=0.02;AFR_AF=0.07;EUR_AF=0.0013 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 3 | 22 | 20000199 | rs183293480 | A | C | 100 | PASS | LDAF=0.0009;THETA=0.0004;AN=2184;AVGPOST=0.9990;VT=SNP;AA=A;RSQ=0.6274;SNPSOURCE=LOWCOV;AC=1;ERATE=0.0003;AF=0.0005;EUR_AF=0.0013 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 4 | 22 | 20000291 | rs185807825 | G | T | 100 | PASS | ERATE=0.0005;AVGPOST=0.9983;AA=G;AN=2184;LDAF=0.0015;VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.5564;AC=2;THETA=0.0003;AF=0.0009;ASN_AF=0.0035 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 5 | 22 | 20000428 | rs55902548 | G | T | 100 | PASS | AC=323;AVGPOST=0.9983;AA=G;AN=2184;VT=SNP;RSQ=0.9949;LDAF=0.1473;SNPSOURCE=LOWCOV;ERATE=0.0003;THETA=0.0003;AF=0.15;ASN_AF=0.0017;AMR_AF=0.15;AFR_AF=0.31;EUR_AF=0.15 | 0 | 0.0 | 326 | 0.8534031413612565 | 326 | 0.14659685863874344 | 0.9970735495519811 |
| 6 | 22 | 20000683 | rs142720028 | A | G | 100 | PASS | AVGPOST=0.9985;AN=2184;LDAF=0.0015;VT=SNP;RSQ=0.5718;AA=A;SNPSOURCE=LOWCOV;THETA=0.0007;ERATE=0.0003;AC=2;AF=0.0009;AFR_AF=0.0041 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 7 | 22 | 20000771 | rs114690707 | A | C | 100 | PASS | ERATE=0.0004;AC=28;AN=2184;RSQ=0.9857;VT=SNP;AA=A;LDAF=0.0130;SNPSOURCE=LOWCOV;AVGPOST=0.9995;THETA=0.0003;AF=0.01;AMR_AF=0.01;AFR_AF=0.05 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 8 | 22 | 20000793 | rs189842693 | T | C | 100 | PASS | ERATE=0.0004;RSQ=0.7411;AA=T;AN=2184;AVGPOST=0.9981;AC=6;VT=SNP;SNPSOURCE=LOWCOV;LDAF=0.0031;THETA=0.0003;AF=0.0027;ASN_AF=0.0035;EUR_AF=0.01 | 0 | 0.0 | 379 | 0.9921465968586387 | 379 | 0.007853403141361256 | 0.990451675899212 |
| 9 | 22 | 20000810 | rs147349046 | C | T | 100 | PASS | AA=C;AVGPOST=0.9994;AC=28;AN=2184;VT=SNP;RSQ=0.9802;SNPSOURCE=LOWCOV;ERATE=0.0003;LDAF=0.0128;THETA=0.0003;AF=0.01;AMR_AF=0.01;AFR_AF=0.05 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 10 | 22 | 20000814 | rs183154520 | T | C | 100 | PASS | ERATE=0.0004;AVGPOST=0.9985;THETA=0.0002;AA=T;AN=2184;RSQ=0.4507;VT=SNP;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0012;AF=0.0005;AMR_AF=0.0028 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 11 | 22 | 20000864 | rs187930998 | G | A | 100 | PASS | AC=7;THETA=0.0014;AA=g;AN=2184;LDAF=0.0037;RSQ=0.8089;VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0006;AVGPOST=0.9982;AF=0.0032;ASN_AF=0.01 | 0 | 0.0 | 381 | 0.9973821989528796 | 381 | 0.002617801047120419 | 0.9989501594289095 |
| 12 | 22 | 20000882 | rs148068532 | C | G | 100 | PASS | THETA=0.0004;AN=2184;AC=8;VT=SNP;RSQ=0.9358;AA=c;LDAF=0.0038;SNPSOURCE=LOWCOV;ERATE=0.0003;AVGPOST=0.9995;AF=0.0037;AMR_AF=0.0028;AFR_AF=0.01 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 13 | 22 | 20000950 | rs1978233 | T | G | 100 | PASS | ERATE=0.0005;AA=G;AN=2184;AC=2157;VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.8667;LDAF=0.9857;AVGPOST=0.9950;THETA=0.0003;AF=0.99;ASN_AF=1.00;AMR_AF=0.98;AFR_AF=1.00;EUR_AF=0.97 | 0 | 0.0 | 13 | 0.034031413612565446 | 369 | 0.034031413612565446 | 0.003297890604959738 |
| 14 | 22 | 20000975 | rs141800233 | G | A | 100 | PASS | ERATE=0.0004;AVGPOST=0.9994;AA=G;AN=2184;THETA=0.0005;VT=SNP;RSQ=0.9593;AC=15;SNPSOURCE=LOWCOV;LDAF=0.0069;AF=0.01;AMR_AF=0.0028;AFR_AF=0.03 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 15 | 22 | 20001001 | rs192051979 | T | C | 100 | PASS | LDAF=0.0027;RSQ=0.6246;AA=T;AN=2184;VT=SNP;ERATE=0.0008;AVGPOST=0.9973;SNPSOURCE=LOWCOV;AC=4;THETA=0.0003;AF=0.0018;ASN_AF=0.01;AMR_AF=0.0028 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 16 | 22 | 20001006 | rs2079702 | G | A | 100 | PASS | ERATE=0.0004;RSQ=0.9917;LDAF=0.8452;THETA=0.0004;AN=2184;AVGPOST=0.9972;VT=SNP;AA=A;AC=1847;SNPSOURCE=LOWCOV;AF=0.85;ASN_AF=0.61;AMR_AF=0.83;AFR_AF=0.99;EUR_AF=0.94 | 0 | 0.0 | 38 | 0.09947643979057591 | 344 | 0.09947643979057591 | 0.421519982305641 |
| 17 | 22 | 20001016 | rs183256914 | C | T | 100 | PASS | AA=C;AN=2184;LDAF=0.0054;AC=6;VT=SNP;ERATE=0.0011;RSQ=0.5737;SNPSOURCE=LOWCOV;THETA=0.0003;AVGPOST=0.9940;AF=0.0027;AMR_AF=0.01;EUR_AF=0.0013 | 0 | 0.0 | 381 | 0.9973821989528796 | 381 | 0.002617801047120419 | 0.9989501594289095 |
| 18 | 22 | 20001157 | rs150580380 | G | A | 100 | PASS | THETA=0.0002;AA=G;AN=2184;VT=SNP;LDAF=0.0020;SNPSOURCE=LOWCOV;AC=1;AVGPOST=0.9968;ERATE=0.0006;RSQ=0.3659;AF=0.0005;ASN_AF=0.0017 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 19 | 22 | 20001159 | rs139570132 | C | T | 100 | PASS | ERATE=0.0004;AA=C;THETA=0.0002;AC=28;RSQ=0.9466;AN=2184;AVGPOST=0.9981;VT=SNP;SNPSOURCE=LOWCOV;LDAF=0.0135;AF=0.01;AMR_AF=0.01;AFR_AF=0.05 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 20 | 22 | 20001219 | rs143369598 | G | C | 100 | PASS | AC=7;AVGPOST=0.9963;THETA=0.0002;AA=G;AN=2184;LDAF=0.0040;VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.6315;ERATE=0.0003;AF=0.0032;ASN_AF=0.01;EUR_AF=0.0026 | 0 | 0.0 | 379 | 0.9921465968586387 | 379 | 0.007853403141361256 | 0.990451675899212 |
| 21 | 22 | 20001333 | rs5993894 | C | T | 100 | PASS | ERATE=0.0004;AA=C;AN=2184;LDAF=0.0528;VT=SNP;AVGPOST=0.9980;SNPSOURCE=LOWCOV;RSQ=0.9854;AC=114;THETA=0.0003;AF=0.05;AMR_AF=0.02;AFR_AF=0.21 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 22 | 22 | 20001434 | rs146344141 | C | T | 100 | PASS | AA=C;THETA=0.0004;AN=2184;VT=SNP;LDAF=0.0101;RSQ=0.9081;SNPSOURCE=LOWCOV;AC=21;ERATE=0.0003;AVGPOST=0.9974;AF=0.01;ASN_AF=0.0017;AMR_AF=0.01;EUR_AF=0.02 | 0 | 0.0 | 375 | 0.981675392670157 | 375 | 0.01832460732984293 | 0.9469376517621076 |
| 23 | 22 | 20001455 | rs188666449 | G | A | 100 | PASS | AVGPOST=0.9986;THETA=0.0004;AA=G;AN=2184;VT=SNP;LDAF=0.0011;SNPSOURCE=LOWCOV;AC=1;RSQ=0.4222;ERATE=0.0003;AF=0.0005;ASN_AF=0.0017 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 24 | 22 | 20001521 | rs139601437 | C | A | 100 | PASS | ERATE=0.0005;AA=C;AN=2184;RSQ=0.5048;LDAF=0.0010;VT=SNP;THETA=0.0006;AVGPOST=0.9989;SNPSOURCE=LOWCOV;AC=1;AF=0.0005;AFR_AF=0.0020 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 25 | 22 | 20001587 | rs71788814 | CAG | C | 530 | PASS | AA=CAG;ERATE=0.0005;AN=2184;AVGPOST=0.9952;VT=INDEL;RSQ=0.9665;LDAF=0.0519;AC=114;THETA=0.0003;AF=0.05;AMR_AF=0.03;AFR_AF=0.21;EUR_AF=0.0013 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 26 | 22 | 20001600 | rs144217522 | T | A | 100 | PASS | ERATE=0.0004;AC=28;AA=T;AN=2184;RSQ=0.9560;VT=SNP;THETA=0.0011;LDAF=0.0126;SNPSOURCE=LOWCOV;AVGPOST=0.9984;AF=0.01;AMR_AF=0.01;AFR_AF=0.05 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 27 | 22 | 20001655 | rs192606530 | G | A | 100 | PASS | ERATE=0.0004;THETA=0.0002;AA=G;AN=2184;RSQ=0.5888;LDAF=0.0018;VT=SNP;SNPSOURCE=LOWCOV;AC=2;AVGPOST=0.9982;AF=0.0009;AMR_AF=0.01 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 28 | 22 | 20001822 | rs111598545 | A | G | 100 | PASS | RSQ=0.9768;THETA=0.0004;AN=2184;VT=SNP;AVGPOST=0.9976;LDAF=0.0418;AA=A;SNPSOURCE=LOWCOV;ERATE=0.0003;AC=91;AF=0.04;ASN_AF=0.01;AMR_AF=0.05;AFR_AF=0.08;EUR_AF=0.04 | 0 | 0.0 | 373 | 0.9764397905759162 | 373 | 0.02356020942408377 | 0.9114585769224057 |
| 29 | 22 | 20002011 | rs184950746 | C | T | 100 | PASS | ERATE=0.0004;AA=C;AVGPOST=0.9994;AN=2184;RSQ=0.6434;THETA=0.0005;VT=SNP;SNPSOURCE=LOWCOV;AC=1;LDAF=0.0008;AF=0.0005;AMR_AF=0.0028 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
| 30 | 22 | 20002207 | rs142461772 | G | A | 100 | PASS | AA=G;AN=2184;AC=6;VT=SNP;AVGPOST=0.9989;LDAF=0.0029;SNPSOURCE=LOWCOV;ERATE=0.0003;THETA=0.0003;RSQ=0.8802;AF=0.0027;AFR_AF=0.01 | 0 | 0.0 | 382 | 1.0 | 382 | 0.0 | 1.0 |
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