{"id":70137,"date":"2026-11-14T23:31:36","date_gmt":"2026-11-14T15:31:36","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=70137"},"modified":"2026-11-14T23:31:36","modified_gmt":"2026-11-14T15:31:36","slug":"gridss2-breakend-inserted-sequences-to-fasta","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/gridss2-breakend-inserted-sequences-to-fasta\/","title":{"rendered":"GRIDSS2 \u5b9e\u8dd1\uff5c\u4e94\u6761\u65ad\u7aef\u8bb0\u5f55\u53ea\u5bfc\u51fa\u56db\u6761\u5e8f\u5217\uff0c\u5c11\u7684\u662f\u54ea\u4e00\u6761\uff1f"},"content":{"rendered":"
\n

\u540c\u4e8b\u4ea4\u6765\u4e00\u4efd\u7ed3\u6784\u53d8\u5f02 VCF\uff0c\u5e0c\u671b\u628a\u65b0\u8fde\u63a5\u5904\u7684\u672a\u77e5\u78b1\u57fa\u63d0\u53d6\u6210 FASTA\uff0c\u518d\u53bb\u505a\u5e8f\u5217\u6bd4\u5bf9\u3002\u770b\u4f3c\u7b80\u5355\uff0c\u5374\u6709\u4e24\u4e2a\u5e38\u89c1\u8bef\u5dee\uff0c\u66ff\u4ee3\u5b57\u7b26\u4e32\u91cc\u542b\u6709\u53c2\u8003\u951a\u70b9\u548c\u8fdc\u7aef\u5750\u6807\uff0c\u4e0d\u80fd\u6574\u4e32\u5f53\u4f5c\u63d2\u5165\u5e8f\u5217\u3002\u4e00\u6761\u7ed3\u6784\u8fde\u63a5\u7684\u4e24\u7aef\u53c8\u53ef\u80fd\u5206\u522b\u4ea7\u751f FASTA \u6761\u76ee\uff0c\u4e0d\u80fd\u62ff\u6761\u76ee\u6570\u5f53\u6210\u4e8b\u4ef6\u6570\u3002\u6211\u4eec\u5b89\u88c5 GRIDSS2 \u7684\u6b63\u5f0f\u53d1\u884c\u5305\uff0c\u7528\u5b83\u81ea\u5df1\u7684\u5e8f\u5217\u5bfc\u51fa\u5de5\u5177\u68c0\u67e5\u4e94\u6761\u8fb9\u754c\u5df2\u77e5\u7684\u65ad\u7aef\u8bb0\u5f55\uff0c\u5e76\u5bf9\u6700\u77ed\u5e8f\u5217\u957f\u5ea6\u505a\u4e86\u56db\u6b21\u5bf9\u7167\u3002<\/p>\n

\u4e00\u4e2a\u65ad\u7aef\u5b57\u7b26\u4e32\u91cc\uff0c\u54ea\u4e9b\u5b57\u7b26\u662f\u78b1\u57fa\u8bc1\u636e<\/h2>\n

VCF \u4e2d\u7684\u65ad\u7aef\u53ef\u4ee5\u53ea\u77e5\u9053\u4e00\u7aef\uff0c\u4f8b\u5982\u5c40\u90e8\u7ec4\u88c5\u5f97\u5230\u4e00\u6bb5\u4f38\u51fa\u5df2\u5b9a\u4f4d\u533a\u57df\u7684\u5e8f\u5217\uff0c\u5374\u65e0\u6cd5\u53ef\u9760\u5b9a\u4f4d\u53e6\u4e00\u7aef\u3002\u5b83\u4e5f\u53ef\u4ee5\u660e\u786e\u5199\u51fa\u53e6\u4e00\u6761\u67d3\u8272\u4f53\u3001\u8fde\u63a5\u4f4d\u7f6e\u53ca\u65b9\u5411\u3002\u524d\u8005\u7684\u66ff\u4ee3\u5b57\u7b26\u4e32\u53ef\u7528\u70b9\u6807\u793a\u672a\u77e5\u65b9\u5411\u7684\u8fdc\u7aef\uff0c\u540e\u8005\u7528\u6210\u5bf9\u65b9\u62ec\u53f7\u5305\u4f4f\u4f19\u4f34\u4f4d\u7f6e\u3002\u8fde\u63a5\u7684\u4e00\u4fa7\u8fd8\u4fdd\u7559\u4e00\u4e2a\u53c2\u8003\u951a\u70b9\uff0c\u4ee5\u4fbf\u56fa\u5b9a\u672c\u5730\u5750\u6807\u3002\u951a\u70b9\u867d\u7136\u662f\u4e00\u4e2a\u771f\u5b9e\u78b1\u57fa\uff0c\u5374\u539f\u672c\u5c31\u5b58\u5728\u539f\u4f4d\uff0c\u4e0d\u80fd\u81ea\u52a8\u7b97\u6210\u65b0\u63d2\u5165\u7684\u4e00\u4e2a\u78b1\u57fa\u3002VCF \u89c4\u8303\u7684\u65ad\u7aef\u8868\u793a<\/a><\/p>\n

GRIDSS2 \u7684\u5bfc\u51fa\u5b50\u7a0b\u5e8f\u8bfb\u53d6\u8fd9\u4e2a\u7ed3\u6784\uff0c\u53d6\u5f97\u8be5\u6761\u65ad\u7aef\u91cc\u663e\u5f0f\u62a5\u544a\u7684\u8fde\u63a5\u5904\u5e8f\u5217\uff0c\u53ea\u6709\u5e8f\u5217\u975e\u7a7a\u4e14\u8fbe\u5230\u7ed9\u5b9a\u957f\u5ea6\u624d\u5199\u5165 FASTA\u3002\u5b83\u662f\u7ed3\u679c\u89e3\u8bfb\u7684\u4e00\u73af\u3002\u672c\u6b21\u8f93\u5165\u662f\u4e3a\u4e86\u68c0\u9a8c\u683c\u5f0f\u89c4\u5219\u800c\u6784\u9020\u7684\u8bb0\u5f55\uff0c\u6574\u4e2a\u5b9e\u9a8c\u4ece\u5df2\u77e5 VCF \u8d77\u6b65\uff0c\u6ca1\u6709\u4ece\u6d4b\u5e8f\u8bfb\u6bb5\u91cd\u65b0\u8fd0\u884c\u65ad\u70b9\u7ec4\u88c5\u3002\u82e5\u7814\u7a76\u7684\u662f\u67d0\u79cd\u771f\u5b9e\u75c5\u6bd2\u63d2\u5165\u6216\u91cd\u590d\u6269\u589e\uff0c\u5bfc\u51fa\u7684\u78b1\u57fa\u672c\u8eab\u4ecd\u9700\u56de\u5230\u539f\u59cb\u7ec4\u88c5\u548c\u8986\u76d6\u8bc1\u636e\u590d\u6838\u3002GRIDSS2 \u53d1\u884c\u7248\u4e2d\u5e8f\u5217\u5bfc\u51fa\u7684\u5b9e\u73b0<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u4ece\u56db\u4efd FASTA \u627e\u56de\u951a\u70b9\u3001\u4f19\u4f34\u4e0e\u957f\u5ea6\u95e8\u69db<\/h2>\n

\u6211\u4eec\u8fd0\u884c GRIDSS2 2.13.2 \u7684 InsertedSequencesToFasta<\/code>\uff0c\u7ed9\u8f93\u5165 VCF \u4fdd\u7559\u4e24\u6761\u67d3\u8272\u4f53\u7684\u5934\u4fe1\u606f\uff0c\u5e76\u7ed9\u6bcf\u884c\u5355\u72ec\u547d\u540d\u3002\u7b2c\u4e00\u884c\u53ea\u6709\u951a\u70b9\u548c\u672a\u77e5\u8fdc\u7aef\u3002\u7b2c\u4e8c\u3001\u7b2c\u56db\u884c\u662f\u5355\u65ad\u7aef\uff0c\u5404\u8bbe\u8ba1\u4e09\u679a\u5f85\u63d0\u53d6\u78b1\u57fa\uff0c\u4f46\u53c2\u8003\u951a\u70b9\u5206\u522b\u5728\u5b57\u7b26\u4e32\u7684\u4e00\u4fa7\u548c\u53e6\u4e00\u4fa7\u3002\u7b2c\u4e09\u3001\u7b2c\u4e94\u884c\u4e92\u76f8\u5217\u4e3a\u4f19\u4f34\uff0c\u5728\u5404\u81ea\u7684\u65ad\u7aef\u63cf\u8ff0\u4e2d\u90fd\u5b89\u6392\u4e86\u76f8\u540c\u7684\u4e24\u78b1\u57fa\u5e8f\u5217\u3002\u6bcf\u6b21\u8fd0\u884c\u53ea\u66f4\u6539\u6700\u77ed\u5e8f\u5217\u957f\u5ea6\uff0c\u72ec\u7acb\u89e3\u6790\u6bcf\u4e2a FASTA \u8bb0\u5f55\u540d\u548c\u5e8f\u5217\u3002GRIDSS2 \u4e0a\u6e38\u7684\u516c\u5f00\u53d1\u884c\u5305<\/a><\/p>\n

\n\n\n\n\n\n\n\n\n
\u8f93\u5165\u8bb0\u5f55<\/th>\nREF \u4e0e ALT<\/th>\n\u6700\u77ed 1 \u6216 2 bp<\/th>\n\u6700\u77ed 3 bp<\/th>\n<\/tr>\n<\/thead>\n
plain<\/td>\nA\uff0cA.<\/td>\n\u65e0\u6761\u76ee<\/td>\n\u65e0\u6761\u76ee<\/td>\n<\/tr>\n
single3<\/td>\nC\uff0cCAGT.<\/td>\nAGT<\/td>\nAGT<\/td>\n<\/tr>\n
other_anchor<\/td>\nT\uff0c.CCTT<\/td>\nCCT<\/td>\nCCT<\/td>\n<\/tr>\n
pairF \u4e0e pairR<\/td>\nG\uff0cGAC[chr2:401[ \uff0f T\uff0c]chr1:202]ACT<\/td>\n\u5404\u8f93\u51fa AC<\/td>\n\u4e24\u8005\u5747\u65e0\u6761\u76ee<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u4e94\u6761\u65ad\u7aef\u80fd\u5bfc\u51fa\u51e0\u6761\u5e8f\u5217\u3002\u7528\u5df2\u77e5\u951a\u70b9\u4e0e\u63d2\u5165\u5e8f\u5217\u7684
\u7528\u5df2\u77e5\u951a\u70b9\u4e0e\u63d2\u5165\u5e8f\u5217\u7684 VCF\uff0c\u8fd0\u884c\u56db\u7ec4\u6700\u77ed\u957f\u5ea6\u6761\u4ef6\u3002<\/figcaption><\/figure>\n

\u6700\u4f4e\u957f\u5ea6\u4e3a\u4e00\u65f6\u5f97\u5230\u56db\u6761\uff0c\u6700\u4f4e\u957f\u5ea6\u4e3a\u4e8c\u65f6\u4ecd\u6709\u56db\u6761\u3002\u4e00\u548c\u4e8c\u95e8\u69db\u4e0b\u7684\u5185\u5bb9\u5b8c\u5168\u76f8\u540c\uff0c\u56e0\u4e3a\u8fd9\u4efd\u8f93\u5165\u6ca1\u6709\u957f\u5ea6\u6070\u4e3a\u4e00\u7684\u65b0\u589e\u5e8f\u5217\u3002\u8c03\u5230\u4e09\u4ee5\u540e\uff0c\u53ea\u6709\u4e24\u4e2a\u5355\u65ad\u7aef\u4fdd\u7559\u4e0b\u6765\u3002\u8c03\u5230\u56db\uff0c\u8f93\u51fa\u6587\u4ef6\u5b58\u5728\uff0c\u4f46\u6ca1\u6709\u4efb\u4f55 FASTA \u6761\u76ee\u3002\u5bf9\u7b2c\u4e00\u884c\u800c\u8a00\uff0c\u70b9\u524d\u7684 A \u4e0e\u53c2\u8003 A \u662f\u540c\u4e00\u4e2a\u951a\u70b9\uff0c\u53bb\u6389\u540e\u6ca1\u6709\u989d\u5916\u5e8f\u5217\uff0c\u6240\u4ee5\u5b83\u5728\u6240\u6709\u8bbe\u7f6e\u4e0b\u90fd\u4e0d\u4f1a\u51fa\u73b0\u3002\u82e5\u4e0b\u6e38\u8bef\u628a\u7a7a\u6587\u4ef6\u5f53\u6210\u7a0b\u5e8f\u5d29\u6e83\uff0c\u53ea\u9700\u5148\u67e5\u9000\u51fa\u72b6\u6001\u3001\u8f93\u5165\u8bb0\u5f55\u6570\u548c\u5404\u6761\u65b0\u589e\u5e8f\u5217\u957f\u5ea6\uff0c\u5c31\u80fd\u5206\u8fa8\u8fc7\u6ee4\u7ed3\u679c\u4e0e\u6267\u884c\u9519\u8bef\u3002<\/p>\n

\u7b2c\u56db\u884c\u5f88\u9002\u5408\u6293\u53d6\u624b\u5199\u89e3\u6790\u5668\u7684\u9519\u8bef\u3002\u5b83\u7684\u66ff\u4ee3\u5b57\u7b26\u4e32\u4ee5\u70b9\u5f00\u5934\uff0c\u7ed3\u5c3e\u5305\u542b\u4e24\u4e2a\u8fde\u7eed\u7684 T\uff0c\u672b\u7aef\u90a3\u4e2a T \u662f\u53c2\u8003\u951a\u70b9\uff0c\u5bfc\u51fa\u7ed3\u679c\u662f CCT\u3002\u82e5\u4e00\u5f8b\u53bb\u6389\u7b2c\u4e00\u4e2a\u78b1\u57fa\uff0c\u4f1a\u8bef\u5220\u5c5e\u4e8e\u65b0\u589e\u5e8f\u5217\u7684 C\uff0c\u540c\u65f6\u7559\u4e0b\u539f\u672c\u5e94\u5254\u9664\u7684\u951a\u70b9\u3002\u6210\u5bf9\u65ad\u7aef\u7684\u4e24\u6761\u8bb0\u5f55\u5219\u8981\u540c\u65f6\u5904\u7406\u62ec\u53f7\u4f4d\u7f6e\u3001\u8fdc\u7aef\u5750\u6807\u548c\u672c\u5730\u53c2\u8003\u78b1\u57fa\u3002\u8fd9\u91cc\u5bfc\u51fa\u7684\u4e24\u4e2a AC \u5404\u81ea\u6cbf\u7528\u8f93\u5165\u8bb0\u5f55\u6807\u8bc6\uff0c\u5373\u4f7f\u5e8f\u5217\u5b8c\u5168\u4e00\u6837\uff0c\u4e5f\u4f9d\u7136\u662f\u4e24\u4e2a\u5e26\u6709\u4e0d\u540c\u6765\u6e90\u6807\u8bc6\u7684\u8f93\u51fa\u3002GRIDSS2 \u5bf9\u65ad\u7aef\u65b9\u5411\u548c\u63d2\u5165\u5e8f\u5217\u7684\u89e3\u6790<\/a><\/p>\n

java -Xmx256m -cp gridss-2.13.2-gridss-jar-with-dependencies.jar \\\r\n  gridss.InsertedSequencesToFasta INPUT=calls.vcf OUTPUT=min3.fa MIN_SEQUENCE_LENGTH=3\r\nawk '\/^>\/{n++} END{print n+0}' min3.fa\r\n<\/code><\/pre>\n
\u8fd8\u53ef\u4ee5\u5bf9\u5bfc\u51fa\u6587\u4ef6\u505a\u4e00\u6b21\u78b1\u57fa\u603b\u91cf\u6838\u7b97\u3002\u95e8\u69db\u4e3a\u4e00\u6216\u4e8c\u65f6\uff0c\u4e24\u6761\u4e09\u78b1\u57fa\u548c\u4e24\u6761\u4e8c\u78b1\u57fa\u76f8\u52a0\uff0c\u603b\u5171\u5341\u4e2a\u78b1\u57fa\u3002\u95e8\u69db\u4e3a\u4e09\u65f6\uff0c\u53ea\u5269\u516d\u4e2a\u78b1\u57fa\uff0c\u8bb0\u5f55\u6570\u51cf\u534a\uff0c\u78b1\u57fa\u6570\u5374\u4fdd\u7559\u4e86\u516d\u6210\u3002\u82e5\u8bfb\u8005\u628a\u201c\u4fdd\u7559\u4e00\u534a\u8bb0\u5f55\u201d\u5199\u6210\u201c\u635f\u5931\u4e00\u534a\u5e8f\u5217\u957f\u5ea6\u201d\uff0c\u5728\u8fd9\u4e2a\u6781\u5c0f\u6837\u4f8b\u4e0a\u5c31\u80fd\u53d1\u73b0\u9519\u8bef\u3002\u9762\u5bf9\u957f\u5ea6\u8de8\u5ea6\u5f88\u5927\u7684\u771f\u5b9e\u63d2\u5165\uff0c\u4e24\u4e2a\u6bd4\u4f8b\u7684\u5dee\u5f02\u4f1a\u66f4\u5927\u3002<\/p>\n
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