Mercurial > repos > miller-lab > snp_analysis_conversion

annotate test-data/vcf2pgSnp_input.vcf @ 3:edf12470a1a6 default tip

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Bugfix from Belinda, in vcf2pgSnp.pl
author Cathy Riemer <cathy+hg@bx.psu.edu>
date Thu, 19 Mar 2015 12:06:34 -0400
parents 35c20b109be5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2
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1 ##fileformat=VCFv4.1
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2 ##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
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3 ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
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4 ##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
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5 ##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
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6 ##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
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7 ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
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8 ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
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9 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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10 ##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
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11 ##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
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12 ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
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13 ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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14 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
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15 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
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16 ##ALT=<ID=DEL,Description="Deletion">
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17 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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18 ##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
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19 ##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
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20 ##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">
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21 ##INFO=<ID=AF,Number=1,Type=Float,Description="Global Allele Frequency based on AC/AN">
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22 ##INFO=<ID=AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
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23 ##INFO=<ID=ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
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24 ##INFO=<ID=AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
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25 ##INFO=<ID=EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
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26 ##INFO=<ID=VT,Number=1,Type=String,Description="indicates what type of variant the line represents">
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27 ##INFO=<ID=SNPSOURCE,Number=.,Type=String,Description="indicates if a snp was called when analysing the low coverage or exome alignment data">
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28 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 HG00099 HG00100
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29 1 10523 . TCCG T 152 PASS VT=INDEL;RSQ=0.5246;ERATE=0.0023;AN=2184;AA=.;THETA=0.0172;AC=5;AVGPOST=0.9954;LDAF=0.0045;AF=0.00;AMR_AF=0.00;AFR_AF=0.01 GT:DS:GL 0|0:0.000:0.00,-1.50,-34.60 0|0:0.000:0.00,-0.90,-20.70 0|0:0.000:0.00,-1.50,-34.50 0|0:0.000:0.00,-0.30,-6.90
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30 1 10583 rs58108140 G A 100 PASS VT=SNP;SNPSOURCE=LOWCOV;AN=2184;AC=327;LDAF=0.2363;AVGPOST=0.7630;ERATE=0.0098;AA=.;RSQ=0.4161;THETA=0.0197;SNPSOURCE=LOWCOV;AF=0.15;ASN_AF=0.15;AMR_AF=0.18;AFR_AF=0.04;EUR_AF=0.21 GT:DS:GL 0|0:0.250:-0.18,-0.47,-2.42 0|0:0.200:-0.24,-0.44,-1.16 0|0:0.250:-0.15,-0.54,-3.12 0|1:0.750:-0.48,-0.48,-0.48
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31 1 10611 rs189107123 C G 100 PASS VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0048;RSQ=0.3814;AN=2184;AVGPOST=0.9427;ERATE=0.0024;LDAF=0.0420;AA=.;SNPSOURCE=LOWCOV;AC=39;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.02 GT:DS:GL 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.350:-0.24,-0.44,-1.16 0|0:0.100:-0.22,-0.42,-1.80 0|0:0.100:-0.48,-0.48,-0.48
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32 1 10616 . CCGCCGTTGCAAAGGCGCGCCG C 2781 PASS VT=INDEL;RSQ=0.1048;AN=2184;LDAF=0.7052;AVGPOST=0.5674;ERATE=0.0146;AA=.;THETA=0.0195;AC=1972;AF=0.90;ASN_AF=0.88;AMR_AF=0.92;AFR_AF=0.89;EUR_AF=0.92 GT:DS:GL 1|1:1.450:0,0,0 1|1:1.750:0,0,0 1|1:1.200:0,0,0 0|1:1.150:0,0,0
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33 1 11540 . T TA 263 PASS VT=INDEL;AVGPOST=0.5915;LDAF=0.2676;AN=2184;RSQ=0.0831;AC=93;THETA=0.0011;AA=.;ERATE=0.0222;AF=0.04;ASN_AF=0.05;AMR_AF=0.04;AFR_AF=0.05;EUR_AF=0.04 GT:DS:GL 0|0:0.700:0,0,0 0|1:0.800:0,0,0 0|0:0.300:0,0,0 0|0:0.450:0,0,0
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34 1 13302 rs180734498 C T 100 PASS VT=SNP;SNPSOURCE=LOWCOV;THETA=0.0159;LDAF=0.1562;AN=2184;AC=250;AA=.;RSQ=0.6272;ERATE=0.0116;SNPSOURCE=LOWCOV;AVGPOST=0.8877;AF=0.11;ASN_AF=0.02;AMR_AF=0.09;AFR_AF=0.21;EUR_AF=0.13 GT:DS:GL 0|0:0.250:-0.13,-0.58,-3.62 0|1:0.950:-2.45,-0.00,-5.00 0|0:0.450:-0.29,-0.32,-5.00 0|0:0.300:-0.48,-0.48,-0.48
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35 1 13327 rs144762171 G C 100 PASS VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.6776;THETA=0.0189;AN=2184;AC=57;AA=.;LDAF=0.0342;AVGPOST=0.9733;SNPSOURCE=LOWCOV;ERATE=0.0007;AF=0.03;ASN_AF=0.01;AMR_AF=0.03;AFR_AF=0.02;EUR_AF=0.04 GT:DS:GL 0|0:0.000:-0.03,-1.11,-5.00 0|1:1.000:-1.97,-0.01,-2.51 0|0:0.050:-0.01,-1.69,-5.00 0|0:0.100:-0.48,-0.48,-0.48
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36 1 13417 . C CGAGA 2788 PASS VT=INDEL;AVGPOST=0.7560;THETA=0.0061;AC=52;AN=2184;AA=.;RSQ=0.1970;LDAF=0.1542;ERATE=0.0127;AF=0.02;ASN_AF=0.02;AMR_AF=0.04;AFR_AF=0.01;EUR_AF=0.03 GT:DS:GL 0|0:0.050:0.00,-0.30,-5.60 0|0:0.250:0,0,0 0|0:0.400:0,0,0 0|0:0.350:0.00,-0.30,-5.60
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37 1 13957 . TC T 226 PASS VT=INDEL;RSQ=0.2600;AN=2184;AA=.;LDAF=0.0542;THETA=0.0144;AVGPOST=0.9144;ERATE=0.0029;AC=27;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.01 GT:DS:GL 0|0:0.150:0,0,0 0|0:0.050:0,0,0 0|0:0.100:0,0,0 0|0:0.100:0,0,0
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38 1 13980 rs151276478 T C 100 PASS VT=SNP;SNPSOURCE=LOWCOV;ERATE=0.0021;THETA=0.0096;RSQ=0.3995;AN=2184;AC=55;LDAF=0.0628;AVGPOST=0.9128;AA=.;SNPSOURCE=LOWCOV;AF=0.03;ASN_AF=0.02;AMR_AF=0.03;AFR_AF=0.01;EUR_AF=0.03 GT:DS:GL 0|0:0.100:-0.48,-0.48,-0.48 0|1:0.950:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48 0|0:0.050:-0.48,-0.48,-0.48
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39 1 16226 . AG A 104 PASS VT=INDEL;THETA=0.0211;AN=2184;RSQ=0.6096;LDAF=0.0034;AVGPOST=0.9971;AA=A;ERATE=0.0008;AC=4;AF=0.00;AMR_AF=0.00;EUR_AF=0.00 GT:DS:GL 0|0:0.000:0.00,-1.50,-24.00 0|0:0.050:0,0,0 0|0:0.000:0.00,-0.30,-4.80 0|0:0.000:0.00,-0.90,-14.40
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40 1 17496 . AC A 209 PASS VT=INDEL;AC=7;AN=2184;ERATE=0.0009;AA=A;RSQ=0.7057;THETA=0.0221;AVGPOST=0.9968;LDAF=0.0045;AF=0.00;AFR_AF=0.01 GT:DS:GL 0|0:0.000:0.00,-3.30,-42.90 0|0:0.000:0,0,0 0|0:0.000:0,0,0 0|0:0.000:0,0,0
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41 1 18869 . ACC A 126 PASS VT=INDEL;LDAF=0.2562;AC=52;AN=2184;ERATE=0.0162;AVGPOST=0.5962;AA=A;RSQ=0.0889;THETA=0.0107;AF=0.02;ASN_AF=0.04;AMR_AF=0.02;AFR_AF=0.02;EUR_AF=0.01 GT:DS:GL 0|0:0.400:0,0,0 0|0:0.350:0,0,0 0|0:0.250:0.00,-0.30,-2.90 0|0:0.550:0,0,0
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42 1 19083 . G GCA 139 PASS VT=INDEL;AVGPOST=0.7121;AN=2184;AC=13;AA=G;THETA=0.0077;ERATE=0.0123;RSQ=0.0826;LDAF=0.1645;AF=0.01;ASN_AF=0.01;AMR_AF=0.01;AFR_AF=0.01;EUR_AF=0.00 GT:DS:GL 0|0:0.200:0,0,0 0|0:0.400:0,0,0 0|0:0.250:0,0,0 0|0:0.350:0,0,0
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43 1 19190 . GC G 815 PASS VT=INDEL;AC=131;LDAF=0.2531;AN=2184;AA=G;THETA=0.0161;AVGPOST=0.6408;RSQ=0.1696;ERATE=0.0188;AF=0.06;ASN_AF=0.05;AMR_AF=0.10;AFR_AF=0.07;EUR_AF=0.04 GT:DS:GL 0|0:0.650:0,0,0 0|0:0.200:0,0,0 0|0:0.650:0,0,0 0|0:0.500:0,0,0
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44 1 20862 . A AG 78 PASS VT=INDEL;ERATE=0.0067;AVGPOST=0.8007;RSQ=0.0827;LDAF=0.8907;AN=2184;THETA=0.0095;AA=A;AC=2178;AF=1.00;ASN_AF=1.00;AMR_AF=1.00;AFR_AF=0.99;EUR_AF=1.00 GT:DS:GL 1|1:1.750:0,0,0 1|1:1.800:0,0,0 1|1:1.850:0,0,0 1|1:1.750:0,0,0
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45 1 30923 rs140337953 G T 100 PASS VT=SNP;SNPSOURCE=LOWCOV;RSQ=0.5363;LDAF=0.6540;THETA=0.0078;AN=2184;AA=T;ERATE=0.0127;AC=1581;SNPSOURCE=LOWCOV;AVGPOST=0.7309;AF=0.72;ASN_AF=0.88;AMR_AF=0.81;AFR_AF=0.48;EUR_AF=0.72 GT:DS:GL 1|1:1.950:-5.00,-0.61,-0.12 0|0:0.450:-0.10,-0.69,-2.81 0|0:0.450:-0.11,-0.64,-3.49 1|1:1.500:-0.48,-0.48,-0.48
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46 1 46402 . C CTGT 104 PASS VT=INDEL;RSQ=0.0943;AA=C;AN=2184;AVGPOST=0.8697;THETA=0.0108;AC=5;LDAF=0.0697;ERATE=0.0056;AF=0.00;ASN_AF=0.00;AMR_AF=0.00;AFR_AF=0.01 GT:DS:GL 0|0:0.050:0,0,0 0|0:0.100:0,0,0 0|0:0.050:0,0,0 0|0:0.050:0,0,0
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47 1 47190 . G GA 868 PASS VT=INDEL;LDAF=0.2298;AN=2184;AC=45;AA=G;RSQ=0.1035;AVGPOST=0.6322;THETA=0.0141;ERATE=0.0127;AF=0.02;ASN_AF=0.00;AMR_AF=0.03;AFR_AF=0.05;EUR_AF=0.01 GT:DS:GL 0|0:0.350:0,0,0 0|0:0.500:0,0,0 0|0:0.550:0,0,0 0|0:0.400:0,0,0
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48 1 49514 . AG A 449 PASS VT=INDEL;THETA=0.0164;AC=52;AN=2184;RSQ=0.4892;AA=A;LDAF=0.0469;AVGPOST=0.9448;ERATE=0.0053;AF=0.02;ASN_AF=0.02;AMR_AF=0.02;AFR_AF=0.01;EUR_AF=0.03 GT:DS:GL 0|0:0.000:0.00,-0.90,-12.40 0|1:0.800:0,0,0 0|0:0.150:-0.10,0.00,0.00 0|0:0.000:0.00,-0.30,-4.20
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49 1 49515 . G GA 44 PASS VT=INDEL;THETA=0.0214;AN=2184;AC=13;AA=A;ERATE=0.0008;AVGPOST=0.9879;LDAF=0.0111;RSQ=0.5361;AF=0.01;ASN_AF=0.02;EUR_AF=0.01 GT:DS:GL 0|0:0.050:0.00,-0.90,-9.70 0|0:0.050:0,0,0 0|0:0.000:0,0,0 0|0:0.000:0.00,-0.30,-3.20
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50 1 50481 . GGT G 2370 PASS VT=INDEL;RSQ=0.3702;THETA=0.0038;AN=2184;AA=G;ERATE=0.0177;AVGPOST=0.7981;AC=142;LDAF=0.1660;AF=0.07;ASN_AF=0.05;AMR_AF=0.13;AFR_AF=0.07;EUR_AF=0.04 GT:DS:GL 0|0:0.250:0,0,0 0|0:0.350:0,0,0 1|0:1.150:-3.00,-0.30,0.00 0|0:0.250:0,0,0