{"id":70111,"date":"2026-11-14T23:13:34","date_gmt":"2026-11-14T15:13:34","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70111"},"modified":"2026-11-14T23:13:34","modified_gmt":"2026-11-14T15:13:34","slug":"freebayes-pooled-alternate-count-fraction-denominators","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/freebayes-pooled-alternate-count-fraction-denominators\/","title":{"rendered":"FreeBayes \u5b9e\u8dd1\uff5c\u540c\u6837\u4e24\u6761\u8bfb\u6bb5\u652f\u6301\u53d8\u5f02\uff0c\u4e3a\u4ec0\u4e48\u4e00\u4e2a\u4f4d\u70b9\u5165\u9009\uff0c\u53e6\u4e00\u4e2a\u88ab\u8fc7\u6ee4\uff1f"},"content":{"rendered":"
\n

\u6269\u589e\u5b50\u6216\u6df7\u6c60\u6d4b\u5e8f\u4e2d\uff0c\u5e38\u89c1\u7684\u63d0\u95ee\u662f\u201c\u4e24\u6761\u66ff\u4ee3\u8bfb\u6bb5\u80fd\u4e0d\u80fd\u7b97\u4e00\u4e2a\u53d8\u5f02\u201d\u3002\u5148\u770b\u5206\u6bcd\u3002\u4e24\u6761\u6765\u81ea\u56db\u6761\u603b\u6df1\u5ea6\uff0c\u89c2\u5bdf\u6bd4\u4f8b\u662f\u4e8c\u5206\u4e4b\u4e00\uff0c\u4e24\u6761\u6765\u81ea\u56db\u5341\u6761\u603b\u6df1\u5ea6\uff0c\u5c31\u53ea\u5360\u767e\u5206\u4e4b\u4e94\u3002\u6211\u4eec\u5728\u540c\u4e00\u4efd BAM \u91cc\u653e\u5165\u8fd9\u4e24\u79cd\u60c5\u51b5\uff0c\u53c8\u6dfb\u52a0\u4e00\u4e2a\u56db\u5341\u6761\u4e2d\u6709\u516b\u6761\u66ff\u4ee3\u7684\u4f4d\u70b9\uff0c\u7528 FreeBayes \u7684\u8fde\u7eed\u6df7\u6c60\u6a21\u5f0f\u9010\u6b21\u8c03\u6574\u5019\u9009\u95e8\u69db\u3002\u56db\u7ec4\u8f93\u51fa\u4e0d\u4ec5\u5c55\u793a\u54ea\u4e9b\u4f4d\u7f6e\u88ab\u7559\u4e0b\uff0c\u8fd8\u7559\u4e0b\u4e00\u4e2a\u5f88\u597d\u7684\u53cd\u4f8b\uff0c\u6709\u4e00\u884c\u660e\u660e\u5199\u51fa\u4e86\u66ff\u4ee3\u78b1\u57fa\uff0c\u57fa\u56e0\u578b\u5b57\u6bb5\u5374\u662f\u53c2\u8003\u7eaf\u5408\u3002<\/p>\n

\u5019\u9009\u53d1\u73b0\u8981\u56de\u7b54\u7684\u4e24\u4e2a\u95ee\u9898<\/h2>\n

FreeBayes \u4ece\u8bfb\u6bb5\u6bd4\u5bf9\u4e2d\u5bfb\u627e\u66ff\u4ee3\u7b49\u4f4d\u7684\u8bc1\u636e\u3002\u6700\u4f4e\u66ff\u4ee3\u89c2\u6d4b\u6570\u7ea6\u675f\u7684\u662f\u201c\u81f3\u5c11\u8981\u770b\u5230\u51e0\u6761\u201d\uff0c\u6700\u4f4e\u66ff\u4ee3\u6bd4\u4f8b\u7ea6\u675f\u7684\u662f\u201c\u76f8\u5bf9\u4e8e\u8be5\u6837\u672c\u53c2\u4e0e\u5224\u65ad\u7684\u89c2\u6d4b\uff0c\u5b83\u5360\u591a\u5c11\u201d\u3002\u8fd9\u4e24\u4e2a\u53c2\u6570\u53ef\u4ee5\u540c\u65f6\u8d77\u4f5c\u7528\u3002\u53ea\u9650\u5236\u6761\u6570\u65f6\uff0c\u6df1\u5ea6\u5f88\u9ad8\u7684\u4f4d\u70b9\u5373\u4f7f\u53ea\u6709\u5f88\u5c0f\u4e00\u90e8\u5206\u8bfb\u6bb5\u51fa\u73b0\u66ff\u4ee3\uff0c\u4e5f\u6709\u53ef\u80fd\u8fdb\u5165\u5019\u9009\u3002\u53ea\u9650\u5236\u6bd4\u4f8b\u65f6\uff0c\u4f4e\u6df1\u5ea6\u4f4d\u7f6e\u7684\u5c11\u6570\u51e0\u6761\u8bfb\u6bb5\u5c31\u53ef\u80fd\u4f7f\u6bd4\u4f8b\u548c\u9884\u671f\u76f8\u5f53\u3002\u5efa\u6a21\u524d\u5148\u628a\u4e24\u9879\u5404\u81ea\u7684\u5206\u6790\u76ee\u7684\u5199\u6e05\u695a\uff0c\u624d\u80fd\u89e3\u91ca\u4e3a\u4ec0\u4e48\u6539\u53d8\u4e00\u4e2a\u53c2\u6570\u4f1a\u4e13\u95e8\u5f71\u54cd\u67d0\u7c7b\u4f4d\u70b9\u3002FreeBayes \u4f5c\u8005\u5bf9\u5019\u9009\u4e0e\u6df7\u6c60\u5206\u6790\u7684\u8bf4\u660e<\/a><\/p>\n

\u672c\u4f8b\u4e3b\u52a8\u9009\u7528\u8fde\u7eed\u6df7\u6c60\u6a21\u5f0f\uff0c\u4ee5\u8bfb\u6bb5\u652f\u6301\u548c\u89c2\u5bdf\u6bd4\u4f8b\u4e3a\u4e3b\u8981\u6559\u5b66\u5bf9\u8c61\u3002\u5728\u8fd9\u6837\u7684\u6a21\u5f0f\u4e0b\uff0c\u8f93\u51fa\u67d0\u884c\u4e0d\u7b49\u4e8e\u5df2\u7ecf\u8bc1\u660e\u5b58\u5728\u4e00\u4e2a\u9ad8\u8d28\u91cf\u4e8c\u500d\u4f53\u6742\u5408\u3002\u6837\u672c\u91cc\u6709\u51e0\u4e2a\u4e2a\u4f53\u3001\u6bcf\u4e2a\u4e2a\u4f53\u8d21\u732e\u662f\u5426\u76f8\u540c\u3001\u8bfb\u6bb5\u662f\u5426\u6765\u81ea\u72ec\u7acb\u5206\u5b50\uff0c\u90fd\u4f1a\u5f71\u54cd\u89c2\u5bdf\u6bd4\u4f8b\u4e0e\u751f\u7269\u5b66\u6bd4\u4f8b\u7684\u5173\u7cfb\u3002\u5982\u679c\u8981\u628a\u7ed3\u679c\u89e3\u91ca\u4e3a\u4e2a\u4f53\u57fa\u56e0\u578b\uff0c\u5e94\u5148\u9009\u62e9\u4e0e\u5b9e\u9645\u500d\u6027\u548c\u5b9e\u9a8c\u5355\u4f4d\u76f8\u5339\u914d\u7684\u6a21\u578b\u3002\u4e0b\u9762\u7684\u4e09\u4e2a\u4f4d\u7f6e\u90fd\u6765\u81ea\u5df2\u77e5\u6784\u9020\uff0c\u4fbf\u4e8e\u628a\u5019\u9009\u662f\u5426\u51fa\u73b0\u4e0e\u6700\u7ec8\u7ed3\u8bba\u5206\u5f00\u68c0\u9a8c\u3002FreeBayes \u5b98\u65b9\u7248\u672c\u4e0e\u53ef\u6267\u884c\u7a0b\u5e8f<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u7528\u4e09\u4e2a\u4f4d\u70b9\u628a\u4e24\u9053\u95e8\u69db\u62c6\u5f00\u770b<\/h2>\n

\u6211\u4eec\u5b89\u88c5 FreeBayes 1.3.10\uff0c\u4eba\u5de5\u751f\u6210\u4e00\u6761\u4e00\u5343\u4e5d\u767e\u78b1\u57fa\u7684\u53c2\u8003\u3002\u6bcf\u6761\u8bfb\u6bb5\u957f\u516b\u5341\u4e2a\u78b1\u57fa\uff0c\u7edf\u4e00\u5b9a\u4f4d\u8d28\u91cf\u548c\u78b1\u57fa\u8d28\u91cf\uff0c\u5728\u6bcf\u4e2a\u76ee\u6807\u9644\u8fd1\u9519\u5f00\u8bfb\u6bb5\u8d77\u70b9\uff0c\u6b63\u53cd\u94fe\u5747\u6709\u89c2\u6d4b\u3002\u53ea\u5728\u8fd9\u4e09\u4e2a\u4e92\u4e0d\u76f8\u90bb\u7684\u4f4d\u7f6e\u63d2\u5165\u6307\u5b9a\u6570\u91cf\u7684\u5355\u78b1\u57fa\u5dee\u5f02\u3002\u8f93\u5165\u5148\u7ecf\u6392\u5e8f\u548c\u5efa\u7d22\u5f15\uff0c\u7136\u540e\u56fa\u5b9a\u53c2\u8003\u3001\u6837\u672c\u4e0e\u5355\u500d\u578b\u957f\u5ea6\u8bbe\u7f6e\uff0c\u5728\u56db\u6b21\u8fd0\u884c\u95f4\u53ea\u6539\u53d8\u6700\u4f4e\u6761\u6570\u6216\u6700\u4f4e\u6bd4\u4f8b\u3002\u4e0b\u8868\u7684\u201c\u5165\u9009\u201d\u662f\u6307\u5728\u5b9e\u9645\u8f93\u51fa VCF \u91cc\u51fa\u73b0\u8fd9\u4e00\u884c\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u6700\u4f4e\u66ff\u4ee3\u6761\u6570\u4e0e\u6bd4\u4f8b<\/th>\n301 \u4f4d\uff0c2\/4<\/th>\n701 \u4f4d\uff0c2\/40<\/th>\n1101 \u4f4d\uff0c8\/40<\/th>\n<\/tr>\n<\/thead>\n
2 \u6761\uff0c20%<\/td>\n\u5165\u9009<\/td>\n\u65e0\u8bb0\u5f55<\/td>\n\u5165\u9009<\/td>\n<\/tr>\n
2 \u6761\uff0c5%<\/td>\n\u5165\u9009<\/td>\n\u5165\u9009<\/td>\n\u5165\u9009<\/td>\n<\/tr>\n
3 \u6761\uff0c5%<\/td>\n\u65e0\u8bb0\u5f55<\/td>\n\u65e0\u8bb0\u5f55<\/td>\n\u5165\u9009<\/td>\n<\/tr>\n
2 \u6761\uff0c21%<\/td>\n\u5165\u9009<\/td>\n\u65e0\u8bb0\u5f55<\/td>\n\u65e0\u8bb0\u5f55<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u4e24\u6761\u66ff\u4ee3\u8bfb\u6bb5\uff0c\u591f\u4e0d\u591f\u3002\u76f8\u540c\u7684\u4e24\u6761\u652f\u6301\u653e\u8fdb\u4e0d\u540c\u6df1\u5ea6\uff0c\u5206\u522b\u8bd5\u56db\u7ec4\u5b9e\u9645\u5019\u9009\u95e8\u69db\u30022
\u76f8\u540c\u7684\u4e24\u6761\u652f\u6301\u653e\u8fdb\u4e0d\u540c\u6df1\u5ea6\uff0c\u5206\u522b\u8bd5\u56db\u7ec4\u5b9e\u9645\u5019\u9009\u95e8\u69db\u3002<\/figcaption><\/figure>\n

\u5f53\u6700\u4f4e\u6761\u6570\u4fdd\u6301\u4e24\u6761\uff0c\u6700\u4f4e\u6bd4\u4f8b\u4ece\u4e8c\u6210\u964d\u5230\u767e\u5206\u4e4b\u4e94\uff0c\u65b0\u589e\u7684\u662f\u7b2c\u4e03\u767e\u96f6\u4e00\u4f4d\u3002\u5b83\u7684\u56db\u5341\u6761\u8bfb\u6bb5\u4e2d\u6709\u4e09\u5341\u516b\u6761\u53c2\u8003\u3001\u4e24\u6761\u66ff\u4ee3\uff0c\u521a\u597d\u8fbe\u5230\u8f83\u4f4e\u6bd4\u4f8b\u3002\u7b2c\u4e00\u4f4d\u539f\u672c\u53ea\u6709\u56db\u6761\u8bfb\u6bb5\uff0c\u5176\u4e2d\u4e24\u6761\u66ff\u4ee3\uff0c\u65e9\u5df2\u8d85\u8fc7\u8f83\u9ad8\u6bd4\u4f8b\u3002\u53cd\u8fc7\u6765\uff0c\u56fa\u5b9a\u767e\u5206\u4e4b\u4e94\u7684\u6bd4\u4f8b\u8981\u6c42\uff0c\u628a\u6700\u4f4e\u6761\u6570\u4ece\u4e24\u6761\u63d0\u5230\u4e09\u6761\uff0c\u524d\u4e24\u5904\u90fd\u6d88\u5931\uff0c\u5373\u4f7f\u7b2c\u4e00\u5904\u7684\u89c2\u5bdf\u6bd4\u4f8b\u9ad8\u8fbe\u4e00\u534a\u3002\u6700\u540e\u628a\u6bd4\u4f8b\u4ece\u767e\u5206\u4e4b\u4e8c\u5341\u63d0\u5230\u767e\u5206\u4e4b\u4e8c\u5341\u4e00\uff0c\u56db\u5341\u6761\u4e2d\u516b\u6761\u66ff\u4ee3\u7684\u4f4d\u7f6e\u9000\u51fa\uff0c\u5c55\u793a\u4e86\u201c\u521a\u5230\u8fb9\u754c\u201d\u548c\u201c\u7a0d\u9ad8\u4e8e\u8fb9\u754c\u201d\u7684\u5b9e\u9645\u533a\u522b\u3002<\/p>\n

\u7b2c\u4e03\u767e\u96f6\u4e00\u4f4d\u5c24\u5176\u503c\u5f97\u6253\u5f00\u6574\u884c\u770b\u3002\u653e\u5bbd\u5230\u4e24\u6761\u3001\u767e\u5206\u4e4b\u4e94\u4ee5\u540e\uff0c\u66ff\u4ee3\u78b1\u57fa A \u88ab\u5199\u51fa\uff0c\u6837\u672c\u5217\u4ecd\u7ed9\u51fa\u96f6\u659c\u7ebf\u96f6\uff0c\u4f4d\u70b9\u8d28\u91cf\u7ea6\u4e3a\u4e8c\u4e58\u5341\u7684\u8d1f\u5341\u56db\u6b21\u65b9\u3002\u4e24\u6761\u66ff\u4ee3\u89c2\u6d4b\u5e76\u6ca1\u6709\u56e0\u4e3a\u51fa\u73b0\u5728 VCF \u4e2d\u5c31\u81ea\u52a8\u5f97\u5230\u9ad8\u7f6e\u4fe1\u5206\u6570\u3002\u7b2c\u4e00\u4e2a\u4f4d\u7f6e\u5728\u76f8\u540c\u53c2\u6570\u4e0b\u8f93\u51fa\u6742\u5408\u6837\u672c\u5b57\u6bb5\uff0c\u4f4d\u70b9\u8d28\u91cf\u7ea6\u4e8c\u5341\u4e03\u70b9\u516d\u3002\u7b2c\u4e09\u5904\u516b\u6761\u66ff\u4ee3\u7684\u4f4d\u70b9\u8d28\u91cf\u7ea6\u516b\u5341\u516b\u70b9\u516b\u3002\u5b83\u4eec\u8ba9\u8bfb\u8005\u5728\u4e00\u4efd\u6587\u4ef6\u91cc\u540c\u65f6\u770b\u5230\u5019\u9009\u95e8\u69db\u3001\u89c2\u6d4b\u6570\u91cf\u548c\u6a21\u578b\u8bc4\u5206\u56de\u7b54\u7684\u662f\u4e0d\u540c\u95ee\u9898\u3002\u628a\u6240\u6709\u6709\u8f93\u51fa\u884c\u7684\u4f4d\u7f6e\u90fd\u5f53\u4f5c\u5df2\u786e\u8ba4\u9633\u6027\uff0c\u4f1a\u62b9\u53bb\u8fd9\u51e0\u9879\u5dee\u5f02\u3002<\/p>\n

freebayes -f ref.fa --pooled-continuous --haplotype-length 0 \\\r\n  --min-alternate-count 2 --min-alternate-fraction 0.05 input.bam > loose.vcf\r\nbcftools query -f '%POS\\t%REF\\t%ALT\\t%QUAL[\\t%GT:%RO:%AO:%DP]\\n' loose.vcf\r\n<\/code><\/pre>\n
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