{"id":70114,"date":"2026-11-14T23:16:41","date_gmt":"2026-11-14T15:16:41","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70114"},"modified":"2026-11-14T23:16:41","modified_gmt":"2026-11-14T15:16:41","slug":"strelka2-somatic-tier1-snv-indel-vaf","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/strelka2-somatic-tier1-snv-indel-vaf\/","title":{"rendered":"Strelka2 \u5b9e\u8dd1\uff5c\u80bf\u7624\u6837\u672c\u6709 8 \u6761\u8bfb\u6bb5\u652f\u6301\u63d2\u5165\uff0c\u4e3a\u4ec0\u4e48\u5206\u6bcd\u53d6 19\uff0c\u4e0d\u53d6\u603b\u6df1\u5ea6 20\uff1f"},"content":{"rendered":"
\n

\u4ece Strelka2 \u7684\u4f53\u7ec6\u80de VCF \u63d0\u53d6\u53d8\u5f02\u7b49\u4f4d\u9891\u7387\uff0c\u5728\u5355\u78b1\u57fa\u66ff\u6362\u4e0a\u5076\u5c14\u80fd\u7528\u201c\u66ff\u4ee3\u6761\u6570\u9664\u4ee5\u603b\u6df1\u5ea6\u201d\u7b97\u51fa\u76f8\u540c\u7b54\u6848\u3002\u6362\u6210\u63d2\u5165\u7f3a\u5931\u5c31\u672a\u5fc5\u5982\u6b64\u3002\u6211\u4eec\u5b89\u88c5\u5386\u53f2\u7248\u672c Strelka2\uff0c\u5b8c\u6574\u8fd0\u884c\u968f\u5305\u7684\u80bf\u7624\u4e0e\u6b63\u5e38\u914d\u5bf9\u793a\u4f8b\u3002\u4e00\u4e2a\u63d2\u5165\u4f4d\u70b9\u5728\u80bf\u7624\u5217\u91cc\u6709\u516b\u6761\u63d2\u5165\u652f\u6301\uff0c\u603b\u6df1\u5ea6\u4e8c\u5341\uff0c\u4f5c\u8005\u63a8\u8350\u7684\u9891\u7387\u7b97\u6cd5\u5374\u662f\u516b\u9664\u4ee5\u5341\u4e5d\uff0c\u7ea6\u767e\u5206\u4e4b\u56db\u5341\u4e8c\u70b9\u4e00\u3002\u8bfb\u61c2\u8fd9\u4e2a\u5dee\u5f02\u9700\u8981\u5f04\u6e05\u4e09\u4e2a\u7ec6\u8282\uff0c\u8f6f\u4ef6\u7ed9\u54ea\u4e9b\u8bc1\u636e\u5355\u8bbe\u5b57\u6bb5\uff0c\u9017\u53f7\u5206\u5f00\u7684\u4e24\u9879\u4ee3\u8868\u4ec0\u4e48\uff0c\u4ee5\u53ca\u5f53\u524d\u770b\u7684\u662f\u54ea\u4e2a\u6837\u672c\u3002<\/p>\n

\u5148\u627e\u5230\u5bf9\u7684\u6587\u4ef6\u548c\u6837\u672c\u5217<\/h2>\n

\u4f53\u7ec6\u80de\u6d41\u7a0b\u4f1a\u5206\u522b\u8f93\u51fa\u5355\u78b1\u57fa\u66ff\u6362\u548c\u63d2\u5165\u7f3a\u5931\u3002\u524d\u8005\u6309\u56db\u79cd\u78b1\u57fa\u5206\u522b\u8bb0\u5f55\u5df2\u7528\u4e8e\u8ba1\u6570\u7684\u89c2\u6d4b\uff0c\u540e\u8005\u5219\u8bb0\u5f55\u660e\u786e\u652f\u6301\u53c2\u8003\u3001\u660e\u786e\u652f\u6301\u76ee\u6807\u63d2\u5165\u7f3a\u5931\u53ca\u5176\u4ed6\u7c7b\u578b\u7684\u89c2\u6d4b\u3002\u89e3\u8bfb\u65f6\u5148\u8bb0\u5f55\u6587\u4ef6\u540d\uff0c\u8bfb VCF \u5934\u91cc\u7684\u6837\u672c\u987a\u5e8f\u4e0e\u5b57\u6bb5\u8bf4\u660e\uff0c\u518d\u6309\u8be5\u884c\u7684\u683c\u5f0f\u5217\u89e3\u6790\u6bcf\u4e2a\u6837\u672c\u3002\u76f8\u540c\u5217\u53f7\u5728\u53e6\u4e00\u4e2a\u6587\u4ef6\u91cc\u4e0d\u4fdd\u8bc1\u4ecd\u662f\u540c\u4e00\u79cd\u8bc1\u636e\u3002\u82e5\u5148\u628a\u4e24\u7c7b\u7ed3\u679c\u8f6c\u6210\u4e00\u5f20\u53ea\u6709\u4f4d\u7f6e\u3001\u66ff\u4ee3\u3001\u6df1\u5ea6\u7684\u8868\uff0c\u65e5\u540e\u5f88\u96be\u6062\u590d\u7a76\u7adf\u91c7\u7528\u4e86\u54ea\u79cd\u9891\u7387\u7b97\u6cd5\u3002Strelka2 \u5b98\u65b9\u624b\u518c\u7684\u8f93\u51fa\u4e0e\u7b49\u4f4d\u9891\u7387\u8bf4\u660e<\/a><\/p>\n

\u8fd9\u4e9b\u8ba1\u6570\u5b57\u6bb5\u5f80\u5f80\u5199\u6210\u4e00\u5bf9\u9017\u53f7\u5206\u9694\u7684\u6574\u6570\u3002\u4e24\u4e2a\u503c\u5bf9\u5e94\u4e0d\u540c\u7684\u8bfb\u6bb5\u7b5b\u9009\u5c42\u7ea7\uff0c\u7b2c\u4e8c\u5c42\u91c7\u7528\u66f4\u5bbd\u677e\u7684\u6761\u4ef6\uff0c\u540c\u4e00\u6761\u8bfb\u6bb5\u53ef\u80fd\u5df2\u7ecf\u5728\u7b2c\u4e00\u5c42\u8ba1\u8fc7\u3002\u5c06\u5b83\u4eec\u76f8\u52a0\u4f1a\u91cd\u590d\u8ba1\u7b97\u5171\u4eab\u7684\u8bfb\u6bb5\u3002\u624b\u518c\u7ed9\u51fa\u7684\u9891\u7387\u4f30\u7b97\u7edf\u4e00\u53d6\u7b2c\u4e00\u5c42\u7684\u660e\u786e\u53c2\u8003\u4e0e\u66ff\u4ee3\u8ba1\u6570\u3002\u8ba1\u7b97\u5f97\u51fa\u7684\u4ecd\u662f\u8fd9\u4e2a\u6837\u672c\u5728\u8fd9\u5957\u89c4\u5219\u4e0b\u7684\u89c2\u5bdf\u6bd4\u4f8b\uff0c\u9700\u8981\u53e6\u5916\u7ed3\u5408\u6df1\u5ea6\u3001\u8d28\u91cf\u3001\u6b63\u5e38\u5bf9\u7167\u548c\u68c0\u6d4b\u8bbe\u8ba1\u5224\u65ad\u5176\u751f\u7269\u5b66\u89e3\u91ca\u3002\u4e0d\u80fd\u628a\u4e00\u4e2a\u6bd4\u4f8b\u76f4\u63a5\u5f53\u4f5c\u80bf\u7624\u7ec6\u80de\u6bd4\u4f8b\uff0c\u7ec4\u7ec7\u6df7\u5408\u548c\u5c40\u90e8\u62f7\u8d1d\u6570\u90fd\u53ef\u80fd\u6539\u53d8\u5b83\u3002<\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u628a\u4e00\u4e2a\u66ff\u6362\u548c\u4e00\u4e2a\u63d2\u5165\u9010\u9879\u624b\u7b97<\/h2>\n

\u6211\u4eec\u4f7f\u7528 Strelka2 2.9.10 \u7684\u5b98\u65b9\u53ef\u6267\u884c\u53d1\u884c\u5305\uff0c\u5728\u9694\u79bb\u7684 Python 2.7 \u73af\u5883\u4e2d\u6267\u884c\u968f\u5305\u7684\u914d\u5bf9\u4f53\u7ec6\u80de\u793a\u4f8b\u3002\u6d41\u7a0b\u5b9e\u9645\u8c03\u7528\u53d8\u5f02\u68c0\u6d4b\u7a0b\u5e8f\uff0c\u540c\u65f6\u5c06\u751f\u6210\u7684\u7ed3\u679c\u4e0e\u5305\u5185\u9884\u671f\u6587\u4ef6\u6bd4\u8f83\uff0c\u6309\u793a\u4f8b\u89c4\u5b9a\u6392\u9664\u8fd0\u884c\u65e5\u671f\u7b49\u53ef\u53d8\u5934\u4fe1\u606f\u540e\uff0c\u6bd4\u8f83\u901a\u8fc7\u3002\u8f93\u51fa\u5305\u542b\u5341\u4e03\u6761\u5355\u78b1\u57fa\u8bb0\u5f55\uff0c\u5341\u516d\u6761\u901a\u8fc7\u3001\u4e00\u6761\u6807\u4e3a\u4f4e\u7ecf\u9a8c\u53d8\u5f02\u8bc4\u5206\u3002\u63d2\u5165\u7f3a\u5931\u5171\u6709\u4e24\u6761\uff0c\u5747\u901a\u8fc7\u3002\u8fd9\u91cc\u4f7f\u7528\u7684\u662f\u6f14\u793a\u53c2\u8003\u4e0a\u7684\u5750\u6807\uff0c\u4e0d\u80fd\u6309\u5b83\u4eec\u53bb\u5b9a\u4f4d\u771f\u5b9e\u60a3\u8005\u7684\u57fa\u56e0\u3002Strelka2 \u5b98\u65b9\u53d1\u884c\u5305<\/a><\/p>\n

\n\n\n\n\n\n\n\n
\u793a\u8303\u4f4d\u70b9<\/th>\n\u80bf\u7624\u7b2c\u4e00\u5c42\u53c2\u8003\u3001\u66ff\u4ee3<\/th>\n\u6b63\u5e38\u7b2c\u4e00\u5c42\u53c2\u8003\u3001\u66ff\u4ee3<\/th>\n\u80bf\u7624\u4e2d\u7684\u8ba1\u7b97<\/th>\n<\/tr>\n<\/thead>\n
demo20 \u7684 991\uff0cC\u2192G<\/td>\n5\u30015<\/td>\n12\u30010<\/td>\n5\/(5+5) = 50%<\/td>\n<\/tr>\n
demo20 \u7684 1148\uff0cC\u2192CTAT<\/td>\n11\u30018<\/td>\n26\u30010<\/td>\n8\/(11+8) = 42.11%<\/td>\n<\/tr>\n
demo20 \u7684 3664\uff0cTC\u2192T<\/td>\n18\u300120<\/td>\n24\u30010<\/td>\n20\/(18+20) = 52.63%<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u516b\u6761\u63d2\u5165\u652f\u6301\uff0c\u5206\u6bcd\u53d6\u51e0\u3002\u8fd0\u884c\u4f5c\u8005\u7684\u914d\u5bf9\u793a\u4f8b\uff0c\u5206\u522b\u4ece
\u8fd0\u884c\u4f5c\u8005\u7684\u914d\u5bf9\u793a\u4f8b\uff0c\u5206\u522b\u4ece SNV \u4e0e indel \u7684\u7b2c\u4e00\u5c42\u8bc1\u636e\u8ba1\u7b97\u3002<\/figcaption><\/figure>\n

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def tier1(value):\r\n    return int(value.split(",")[0])\r\n\r\ndef observed_fraction(sample, ref, alt, is_snv):\r\n    ref_key, alt_key = (ref + "U", alt + "U") if is_snv else ("TAR", "TIR")\r\n    support_ref = tier1(sample[ref_key])\r\n    support_alt = tier1(sample[alt_key])\r\n    depth = support_ref + support_alt\r\n    return support_alt \/ depth if depth else None\r\n<\/code><\/pre>\n
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