{"id":1514,"date":"2013-06-13T11:05:50","date_gmt":"2013-06-13T03:05:50","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1514"},"modified":"2013-06-14T10:17:45","modified_gmt":"2013-06-14T02:17:45","slug":"vcf%e6%a0%bc%e5%bc%8f%e8%af%a6%e8%a7%a3","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1514","title":{"rendered":"VCF\u683c\u5f0f\u8be6\u89e3"},"content":{"rendered":"<p>VCF\u683c\u5f0f\uff1aVriant Call Format.\u5173\u4e8e\u5176\u8be6\u7ec6\u63cf\u8ff0\uff0c\u8bf7\u89c1GATK\u7684FAQ\uff1a<a href=\"http:\/\/gatkforums.broadinstitute.org\/discussion\/1268\/how-should-i-interpret-vcf-files-produced-by-the-gatk\" target=\"_blank\">How should I interpret VCF files produced by the GATK?<\/a><\/p>\n<h1>1. \u4ec0\u4e48\u662fVCF\uff1f<\/h1>\n<p>CVF\u662f\u7528\u4e8e\u63cf\u8ff0SNP\uff0cINDEL\u548cSV\u7ed3\u679c\u7684\u6587\u672c\u6587\u4ef6\u3002\u5728GATK\u8f6f\u4ef6\u4e2d\u5f97\u5230\u6700\u597d\u7684\u652f\u6301\uff0c\u5f53\u7136SAMtools\u5f97\u5230\u7684\u7ed3\u679c\u4e5f\u662fCVF\u683c\u5f0f\uff0c\u548cGATK\u7684CVF\u683c\u5f0f\u6709\u70b9\u5dee\u522b\u3002<\/p>\n<h1>2. VCF\u7684\u4e3b\u4f53\u7ed3\u6784<\/h1>\n<p>\u5148\u7ed9\u51fa\u4e00\u4e2aVCF\u6587\u4ef6\u7684\u8303\u4f8b\uff1a<\/p>\n<pre><code>##fileformat=VCFv4.0\r\n##FILTER=&lt;ID=LowQual,Description=\"QUAL &lt; 50.0\"&gt;\r\n##FORMAT=&lt;ID=AD,Number=.,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\"&gt;\r\n##FORMAT=&lt;ID=DP,Number=1,Type=Integer,Description=\"Read Depth (only filtered reads used for calling)\"&gt;\r\n##FORMAT=&lt;ID=GQ,Number=1,Type=Float,Description=\"Genotype Quality\"&gt;\r\n##FORMAT=&lt;ID=GT,Number=1,Type=String,Description=\"Genotype\"&gt;\r\n##FORMAT=&lt;ID=PL,Number=3,Type=Float,Description=\"Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic\"&gt;\r\n##INFO=&lt;ID=AC,Number=.,Type=Integer,Description=\"Allele count in genotypes, for each ALT allele, in the same order as listed\"&gt;\r\n##INFO=&lt;ID=AF,Number=.,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\"&gt;\r\n##INFO=&lt;ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\"&gt;\r\n##INFO=&lt;ID=DB,Number=0,Type=Flag,Description=\"dbSNP Membership\"&gt;\r\n##INFO=&lt;ID=DP,Number=1,Type=Integer,Description=\"Total Depth\"&gt;\r\n##INFO=&lt;ID=DS,Number=0,Type=Flag,Description=\"Were any of the samples downsampled?\"&gt;\r\n##INFO=&lt;ID=Dels,Number=1,Type=Float,Description=\"Fraction of Reads Containing Spanning Deletions\"&gt;\r\n##INFO=&lt;ID=HRun,Number=1,Type=Integer,Description=\"Largest Contiguous Homopolymer Run of Variant Allele In Either Direction\"&gt;\r\n##INFO=&lt;ID=HaplotypeScore,Number=1,Type=Float,Description=\"Consistency of the site with two (and only two) segregating haplotypes\"&gt;\r\n##INFO=&lt;ID=MQ,Number=1,Type=Float,Description=\"RMS Mapping Quality\"&gt;\r\n##INFO=&lt;ID=MQ0,Number=1,Type=Integer,Description=\"Total Mapping Quality Zero Reads\"&gt;\r\n##INFO=&lt;ID=QD,Number=1,Type=Float,Description=\"Variant Confidence\/Quality by Depth\"&gt;\r\n##INFO=&lt;ID=SB,Number=1,Type=Float,Description=\"Strand Bias\"&gt;\r\n##INFO=&lt;ID=VQSLOD,Number=1,Type=Float,Description=\"log10-scaled probability of variant being true under the trained gaussian mixture model\"&gt;\r\n##UnifiedGenotyperV2=\"analysis_type=UnifiedGenotyperV2 input_file=[TEXT CLIPPED FOR CLARITY]\"\r\n#CHROM  POS ID      REF ALT QUAL    FILTER  INFO    FORMAT  NA12878\r\nchr1    873762  .       T   G   5231.78 PASS    AC=1;AF=0.50;AN=2;DP=315;Dels=0.00;HRun=2;HaplotypeScore=15.11;MQ=91.05;MQ0=15;QD=16.61;SB=-1533.02;VQSLOD=-1.5473 GT:AD:DP:GQ:PL   0\/1:173,141:282:99:255,0,255\r\nchr1    877664  rs3828047   A   G   3931.66 PASS    AC=2;AF=1.00;AN=2;DB;DP=105;Dels=0.00;HRun=1;HaplotypeScore=1.59;MQ=92.52;MQ0=4;QD=37.44;SB=-1152.13;VQSLOD= 0.1185 GT:AD:DP:GQ:PL  1\/1:0,105:94:99:255,255,0\r\nchr1    899282  rs28548431  C   T   71.77   PASS    AC=1;AF=0.50;AN=2;DB;DP=4;Dels=0.00;HRun=0;HaplotypeScore=0.00;MQ=99.00;MQ0=0;QD=17.94;SB=-46.55;VQSLOD=-1.9148 GT:AD:DP:GQ:PL  0\/1:1,3:4:25.92:103,0,26\r\nchr1    974165  rs9442391   T   C   29.84   LowQual AC=1;AF=0.50;AN=2;DB;DP=18;Dels=0.00;HRun=1;HaplotypeScore=0.16;MQ=95.26;MQ0=0;QD=1.66;SB=-0.98 GT:AD:DP:GQ:PL  0\/1:14,4:14:60.91:61,0,255<\/code><\/pre>\n<p>\u4ece\u8303\u4f8b\u4e0a\u770b\uff0cVCF\u6587\u4ef6\u5206\u4e3a\u4e24\u90e8\u5206\u5185\u5bb9\uff1a\u4ee5\u201c#\u201d\u5f00\u5934\u7684\u6ce8\u91ca\u90e8\u5206\uff1b\u6ca1\u6709\u201c#\u201d\u5f00\u5934\u7684\u4e3b\u4f53\u90e8\u5206\u3002<\/p>\n<p>\u503c\u5f97\u6ce8\u610f\u7684\u662f\uff0c\u6ce8\u91ca\u90e8\u5206\u6709\u5f88\u591a\u5bf9VCF\u7684\u4ecb\u7ecd\u4fe1\u606f\u3002\u5b9e\u9645\u4e0a\u4e0d\u9700\u8981\u672c\u6587\u7ae0\uff0c\u53ea\u662f\u770b\u770b\u8fd9\u4e2a\u6ce8\u91ca\u90e8\u5206\u5c31\u5b8c\u5168\u660e\u767d\u4e86VCF\u5404\u884c\u5404\u5217\u4ee3\u8868\u7684\u610f\u4e49\u3002\u6211\u4eec\u5148\u8bb2VCF\u6587\u4ef6\u4e3b\u9898\u90e8\u5206\u7684\u7ed3\u6784\uff0c\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n<pre>[HEADER LINES]\r\n#CHROM  POS ID      REF ALT QUAL    FILTER  INFO          FORMAT          NA12878\r\nchr1    873762  .       T   G   5231.78 PASS    [ANNOTATIONS] GT:AD:DP:GQ:PL  0\/1:173,141:282:99:255,0,255\r\nchr1    877664  rs3828047   A   G   3931.66 PASS    [ANNOTATIONS] GT:AD:DP:GQ:PL  1\/1:0,105:94:99:255,255,0\r\nchr1    899282  rs28548431  C   T   71.77   PASS    [ANNOTATIONS] GT:AD:DP:GQ:PL  0\/1:1,3:4:25.92:103,0,26\r\nchr1    974165  rs9442391   T   C   29.84   LowQual [ANNOTATIONS] GT:AD:DP:GQ:PL  0\/1:14,4:14:60.91:61,0,255<\/pre>\n<p>\u4ee5\u4e0a\u53bb\u6389\u4e86\u5934\u90e8\u7684\u6ce8\u91ca\u884c\uff0c\u53ea\u7559\u4e0b\u4e86\u4ee3\u8868\u6bcf\u4e00\u884c\u610f\u4e49\u7684\u6ce8\u91ca\u884c\u3002\u4e3b\u4f53\u90e8\u5206\u4e2d\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2aVariant\u7684\u4fe1\u606f\u3002<\/p>\n<h1>3. \u600e\u4e48\u89e3\u91caVariation<\/h1>\n<p><span style=\"color: #ff00ff;\">CHROM \u548c POS\uff1a<\/span>\u4ee3\u8868\u53c2\u8003\u5e8f\u5217\u540d\u548cvariant\u7684\u4f4d\u7f6e\uff1b\u5982\u679c\u662fINDEL\u7684\u8bdd\uff0c\u4f4d\u7f6e\u662fINDEL\u7684\u7b2c\u4e00\u4e2a\u78b1\u57fa\u4f4d\u7f6e\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">ID\uff1a<\/span>variant\u7684ID\u3002\u6bd4\u5982\u5728dbSNP\u4e2d\u6709\u8be5SNP\u7684id\uff0c\u5219\u4f1a\u5728\u6b64\u884c\u7ed9\u51fa\uff1b\u82e5\u6ca1\u6709\uff0c\u5219\u7528&#8217;.&#8217;\u8868\u793a\u5176\u4e3a\u4e00\u4e2anovel variant\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">REF \u548c ALT\uff1a<\/span>\u53c2\u8003\u5e8f\u5217\u7684\u78b1\u57fa \u548c Variant\u7684\u78b1\u57fa\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">QUAL\uff1a<\/span>Phred\u683c\u5f0f(Phred_scaled)\u7684\u8d28\u91cf\u503c\uff0c\u8868\u793a\u5728\u8be5\u4f4d\u70b9\u5b58\u5728variant\u7684\u53ef\u80fd\u6027\uff1b\u8be5\u503c\u8d8a\u9ad8\uff0c\u5219variant\u7684\u53ef\u80fd\u6027\u8d8a\u5927\uff1b\u8ba1\u7b97\u65b9\u6cd5\uff1aPhred\u503c = -10 * log (1-p) p\u4e3avariant\u5b58\u5728\u7684\u6982\u7387; \u901a\u8fc7\u8ba1\u7b97\u516c\u5f0f\u53ef\u4ee5\u770b\u51fa\u503c\u4e3a10\u7684\u8868\u793a\u9519\u8bef\u6982\u7387\u4e3a0.1\uff0c\u8be5\u4f4d\u70b9\u4e3avariant\u7684\u6982\u7387\u4e3a90%\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">FILTER\uff1a<\/span>\u4f7f\u7528\u4e0a\u4e00\u4e2aQUAL\u503c\u6765\u8fdb\u884c\u8fc7\u6ee4\u7684\u8bdd\uff0c\u662f\u4e0d\u591f\u7684\u3002GATK\u80fd\u4f7f\u7528\u5176\u5b83\u7684\u65b9\u6cd5\u6765\u8fdb\u884c\u8fc7\u6ee4\uff0c\u8fc7\u6ee4\u7ed3\u679c\u4e2d\u901a\u8fc7\u5219\u8be5\u503c\u4e3a&#8221;PASS&#8221;;\u82e5variant\u4e0d\u53ef\u9760\uff0c\u5219\u8be5\u9879\u4e0d\u4e3a&#8221;PASS&#8221;\u6216&#8221;.&#8221;\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">INFO\uff1a<\/span> \u8fd9\u4e00\u884c\u662fvariant\u7684\u8be6\u7ec6\u4fe1\u606f\uff0c\u5185\u5bb9\u5f88\u591a\uff0c\u4ee5\u4e0b\u518d\u5177\u4f53\u8be6\u8ff0\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">FORMAT \u548c NA12878\uff1a<\/span>\u8fd9\u4e24\u884c\u5408\u8d77\u6765\u63d0\u4f9b\u4e86&#8217;NA12878&#8217;\u8fd9\u4e2asample\u7684\u57fa\u56e0\u578b\u7684\u4fe1\u606f\u3002&#8217;NA12878&#8217;\u4ee3\u8868\u8fd9\u8be5\u540d\u79f0\u7684\u6837\u54c1\uff0c\u662f\u7531BAM\u6587\u4ef6\u4e2d\u7684@RG\u4e0b\u7684 SM \u6807\u7b7e\u51b3\u5b9a\u7684\u3002<\/p>\n<h1>4. \u57fa\u56e0\u578b\u4fe1\u606f<\/h1>\n<pre>chr1    873762  .       T   G   [CLIPPED] GT:AD:DP:GQ:PL    0\/1:173,141:282:99:255,0,255\r\nchr1    877664  rs3828047   A   G   [CLIPPED] GT:AD:DP:GQ:PL    1\/1:0,105:94:99:255,255,0\r\nchr1    899282  rs28548431  C   T   [CLIPPED] GT:AD:DP:GQ:PL    0\/1:1,3:4:25.92:103,0,26<\/pre>\n<p>\u770b\u4e0a\u9762\u6700\u540e\u4e24\u5217\u6570\u636e\uff0c\u8fd9\u4e24\u5217\u6570\u636e\u662f\u5bf9\u5e94\u7684\uff0c\u524d\u8005\u4e3a\u683c\u5f0f\uff0c\u540e\u8005\u4e3a\u683c\u5f0f\u5bf9\u5e94\u7684\u6570\u636e\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">GT\uff1a<\/span>\u6837\u54c1\u7684\u57fa\u56e0\u578b\uff08genotype\uff09\u3002\u4e24\u4e2a\u6570\u5b57\u4e2d\u95f4\u7528&#8217;\/&#8217;\u5206\u5f00\uff0c\u8fd9\u4e24\u4e2a\u6570\u5b57\u8868\u793a\u53cc\u500d\u4f53\u7684sample\u7684\u57fa\u56e0\u578b\u30020 \u8868\u793a\u6837\u54c1\u4e2d\u6709ref\u7684allele\uff1b 1 \u8868\u793a\u6837\u54c1\u4e2dvariant\u7684allele\uff1b 2\u8868\u793a\u6709\u7b2c\u4e8c\u4e2avariant\u7684allele\u3002\u56e0\u6b64\uff1a 0\/0 \u8868\u793asample\u4e2d\u8be5\u4f4d\u70b9\u4e3a\u7eaf\u5408\u7684\uff0c\u548cref\u4e00\u81f4\uff1b 0\/1 \u8868\u793asample\u4e2d\u8be5\u4f4d\u70b9\u4e3a\u6742\u5408\u7684\uff0c\u6709ref\u548cvariant\u4e24\u4e2a\u57fa\u56e0\u578b\uff1b 1\/1 \u8868\u793asample\u4e2d\u8be5\u4f4d\u70b9\u4e3a\u7eaf\u5408\u7684\uff0c\u548cvariant\u4e00\u81f4\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">AD \u548c DP\uff1a<\/span>AD(Allele Depth)\u4e3asample\u4e2d\u6bcf\u4e00\u79cdallele\u7684reads\u8986\u76d6\u5ea6,\u5728diploid\u4e2d\u5219\u662f\u7528\u9017\u53f7\u5206\u5272\u7684\u4e24\u4e2a\u503c\uff0c\u524d\u8005\u5bf9\u5e94ref\u57fa\u56e0\u578b\uff0c\u540e\u8005\u5bf9\u5e94variant\u57fa\u56e0\u578b\uff1b DP\uff08Depth\uff09\u4e3asample\u4e2d\u8be5\u4f4d\u70b9\u7684\u8986\u76d6\u5ea6\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">GQ\uff1a<\/span>\u57fa\u56e0\u578b\u7684\u8d28\u91cf\u503c(Genotype Quality)\u3002Phred\u683c\u5f0f(Phred_scaled)\u7684\u8d28\u91cf\u503c\uff0c\u8868\u793a\u5728\u8be5\u4f4d\u70b9\u8be5\u57fa\u56e0\u578b\u5b58\u5728\u7684\u53ef\u80fd\u6027\uff1b\u8be5\u503c\u8d8a\u9ad8\uff0c\u5219Genotype\u7684\u53ef\u80fd\u6027\u8d8a\u5927\uff1b\u8ba1\u7b97\u65b9\u6cd5\uff1aPhred\u503c = -10 * log (1-p) p\u4e3a\u57fa\u56e0\u578b\u5b58\u5728\u7684\u6982\u7387\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">PL\uff1a<\/span>\u6307\u5b9a\u7684\u4e09\u79cd\u57fa\u56e0\u578b\u7684\u8d28\u91cf\u503c(provieds the likelihoods of the given genotypes)\u3002\u8fd9\u4e09\u79cd\u6307\u5b9a\u7684\u57fa\u56e0\u578b\u4e3a(0\/0,0\/1,1\/1)\uff0c\u8fd9\u4e09\u79cd\u57fa\u56e0\u578b\u7684\u6982\u7387\u603b\u548c\u4e3a1\u3002\u548c\u4e4b\u524d\u4e0d\u4e00\u81f4\uff0c\u8be5\u503c\u8d8a\u5927\uff0c\u8868\u660e\u4e3a\u8be5\u79cd\u57fa\u56e0\u578b\u7684\u53ef\u80fd\u6027\u8d8a\u5c0f\u3002 Phred\u503c = -10 * log (p) p\u4e3a\u57fa\u56e0\u578b\u5b58\u5728\u7684\u6982\u7387\u3002<\/p>\n<h1>5. VCF\u7b2c8\u5217\u7684\u4fe1\u606f<\/h1>\n<p>\u8be5\u5217\u4fe1\u606f\u6700\u591a\u4e86\uff0c\u90fd\u662f\u4ee5 &#8220;TAG=Value&#8221;,\u5e76\u4f7f\u7528&#8221;;&#8221;\u5206\u9694\u7684\u5f62\u5f0f\u3002\u5176\u4e2d\u5f88\u591a\u7684\u6ce8\u91ca\u4fe1\u606f\u5728VCF\u6587\u4ef6\u7684\u5934\u90e8\u6ce8\u91ca\u4e2d\u7ed9\u51fa\u3002\u4ee5\u4e0b\u662f\u8fd9\u4e9bTAG\u7684\u89e3\u91ca<\/p>\n<p><span style=\"color: #ff00ff;\">AC\uff0cAF \u548c AN\uff1a<\/span>AC(Allele Count) \u8868\u793a\u8be5Allele\u7684\u6570\u76ee\uff1bAF(Allele Frequency) \u8868\u793aAllele\u7684\u9891\u7387\uff1b AN(Allele Number) \u8868\u793aAllele\u7684\u603b\u6570\u76ee\u3002\u5bf9\u4e8e1\u4e2adiploid sample\u800c\u8a00\uff1a\u5219\u57fa\u56e0\u578b 0\/1 \u8868\u793asample\u4e3a\u6742\u5408\u5b50\uff0cAllele\u6570\u4e3a1(\u53cc\u500d\u4f53\u7684sample\u5728\u8be5\u4f4d\u70b9\u53ea\u67091\u4e2a\u7b49\u4f4d\u57fa\u56e0\u53d1\u751f\u4e86\u7a81\u53d8)\uff0cAllele\u7684\u9891\u7387\u4e3a0.5(\u53cc\u500d\u4f53\u7684sample\u5728\u8be5\u4f4d\u70b9\u53ea\u670950%\u7684\u7b49\u4f4d\u57fa\u56e0\u53d1\u751f\u4e86\u7a81\u53d8)\uff0c\u603b\u7684Allele\u4e3a2\uff1b \u57fa\u56e0\u578b 1\/1 \u5219\u8868\u793asample\u4e3a\u7eaf\u5408\u7684\uff0cAllele\u6570\u4e3a2\uff0cAllele\u7684\u9891\u7387\u4e3a1\uff0c\u603b\u7684Allele\u4e3a2\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">DP\uff1a<\/span>reads\u8986\u76d6\u5ea6\u3002\u662f\u4e00\u4e9breads\u88ab\u8fc7\u6ee4\u6389\u540e\u7684\u8986\u76d6\u5ea6\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">Dels\uff1a<\/span>Fraction of Reads Containing Spanning Deletions\u3002\u8fdb\u884cSNP\u548cINDEL calling\u7684\u7ed3\u679c\u4e2d\uff0c\u6709\u8be5TAG\u5e76\u4e14\u503c\u4e3a0\u8868\u793a\u8be5\u4f4d\u70b9\u4e3aSNP\uff0c\u6ca1\u6709\u5219\u4e3aINDEL\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">FS\uff1a<\/span>\u4f7f\u7528Fisher&#8217;s\u7cbe\u786e\u68c0\u9a8c\u6765\u68c0\u6d4bstrand bias\u800c\u5f97\u5230\u7684Fhred\u683c\u5f0f\u7684p\u503c\u3002\u8be5\u503c\u8d8a\u5c0f\u8d8a\u597d\u3002\u4e00\u822c\u8fdb\u884cfilter\u7684\u65f6\u5019\uff0c\u53ef\u4ee5\u8bbe\u7f6e FS &lt; 10\uff5e20\u3002<\/p>\n<p><span style=\"color: #ff00ff;\">HaplotypeScore\uff1a<\/span>Consistency of the site with at most two segregating haplotypes<\/p>\n<p><span style=\"color: #ff00ff;\">InbreedingCoeff\uff1a<\/span>Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hard-Weinberg expectation<\/p>\n<p><span style=\"color: #ff00ff;\">MLEAC\uff1a<\/span>Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed<\/p>\n<p><span style=\"color: #ff00ff;\">MLEAF\uff1a<\/span>Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT alle in the same order as listed<\/p>\n<p><span style=\"color: #ff00ff;\">MQ\uff1a<\/span>RMS Mapping Quality<\/p>\n<p><span style=\"color: #ff00ff;\">MQ0\uff1a<\/span>Total Mapping Quality Zero Reads<\/p>\n<p><span style=\"color: #ff00ff;\">MQRankSum\uff1a<\/span>Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities<\/p>\n<p><span style=\"color: #ff00ff;\">QD\uff1a<\/span>Variant Confidence\/Quality by Depth<\/p>\n<p><span style=\"color: #ff00ff;\">RPA\uff1a<\/span>Number of times tandem repeat unit is repeated, for each allele (including reference)<\/p>\n<p><span style=\"color: #ff00ff;\">RU\uff1a<\/span>Tandem repeat unit (bases)<\/p>\n<p><span style=\"color: #ff00ff;\">ReadPosRankSum\uff1a<\/span>Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias<\/p>\n<p><span style=\"color: #ff00ff;\">STR\uff1a<\/span>Variant is a short tandem repeat<\/p>\n","protected":false},"excerpt":{"rendered":"<p>VCF\u683c\u5f0f\uff1aVriant Call Format.\u5173\u4e8e\u5176\u8be6\u7ec6\u63cf\u8ff0\uff0c\u8bf7\u89c1GATK\u7684 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=1514\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1514"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=1514"}],"version-history":[{"count":9,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1514\/revisions"}],"predecessor-version":[{"id":1599,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1514\/revisions\/1599"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1514"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1514"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1514"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}