{"id":71411,"date":"2026-11-15T00:49:57","date_gmt":"2026-11-14T16:49:57","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=71411"},"modified":"2026-11-15T01:14:52","modified_gmt":"2026-11-14T17:14:52","slug":"sniffles2-joint-sv-called-reference-versus-no-coverage","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/sniffles2-joint-sv-called-reference-versus-no-coverage\/","title":{"rendered":"Sniffles2 \u5b9e\u8dd1\uff5c\u4e24\u4e2a\u6837\u672c\u90fd\u6ca1\u62a5\u7f3a\u5931\uff0c\u4e3a\u4ec0\u4e48\u8054\u5408\u5206\u578b\u4e00\u4e2a\u662f 0\/0\uff0c\u4e00\u4e2a\u662f .\/.\uff1f"},"content":{"rendered":"
\n

\u5047\u8bbe\u4f60\u5728\u4e00\u4e2a\u6837\u672c\u4e2d\u53d1\u73b0\u4e00\u6bb5\u4e09\u767e\u516d\u5341\u78b1\u57fa\u7684\u7f3a\u5931\uff0c\u53e6\u5916\u4e24\u4efd\u5355\u6837\u672c\u53d8\u5f02\u8868\u5728\u540c\u4e00\u4f4d\u7f6e\u90fd\u662f\u7a7a\u767d\u3002\u73b0\u5728\u8981\u8ba1\u7b97\u8fd9\u6bb5\u7f3a\u5931\u5728\u961f\u5217\u4e2d\u7684\u9891\u7387\uff0c\u80fd\u76f4\u63a5\u628a\u4e09\u4e2a\u4eba\u90fd\u653e\u8fdb\u5206\u6bcd\u5417\uff1f\u6211\u4eec\u6a21\u62df\u4e86\u4e09\u4e2a\u6709\u5df2\u77e5\u771f\u503c\u7684\u6837\u672c\uff0c\u5b9e\u9645\u5b89\u88c5 Sniffles2\uff0c\u5206\u522b\u8fd0\u884c\u5355\u6837\u672c\u53d1\u73b0\u548c\u591a\u6837\u672c\u8054\u5408\u5206\u6790\u3002\u4e24\u4e2a\u5355\u6837\u672c\u6587\u4ef6\u770b\u8d77\u6765\u4e00\u6837\u5b89\u9759\uff0c\u628a\u5b83\u4eec\u7684\u5c40\u90e8\u8986\u76d6\u5e26\u8fdb\u8054\u5408\u5206\u578b\u540e\uff0c\u80fd\u652f\u6301\u7684\u5224\u65ad\u5374\u5b8c\u5168\u4e0d\u540c\u3002Sniffles2 \u5b98\u65b9\u5de5\u4f5c\u6d41\u7a0b<\/a><\/p>\n

\u7a7a\u767d\u884c\u6f0f\u6389\u7684\u90a3\u90e8\u5206\u4fe1\u606f<\/h2>\n

\u957f\u8bfb\u957f\u7ed3\u6784\u53d8\u5f02\u5206\u6790\u5148\u4ece\u6bd4\u5bf9\u4e2d\u5bfb\u627e\u652f\u6301\u63d2\u5165\u3001\u7f3a\u5931\u6216\u5176\u4ed6\u4e8b\u4ef6\u7684\u8bfb\u6bb5\uff0c\u518d\u628a\u540c\u4e00\u4e8b\u4ef6\u9644\u8fd1\u7684\u8bc1\u636e\u805a\u8d77\u6765\u3002\u5355\u6837\u672c\u53d8\u5f02\u6587\u4ef6\u901a\u5e38\u53ea\u8bb0\u5f55\u901a\u8fc7\u76f8\u5e94\u6761\u4ef6\u7684\u4e8b\u4ef6\u3002\u4e00\u4e2a\u4f4d\u7f6e\u6ca1\u6709\u8bb0\u5f55\uff0c\u53ef\u80fd\u56e0\u4e3a\u6709\u8db3\u591f\u8bfb\u6bb5\u6309\u53c2\u8003\u5e8f\u5217\u987a\u5229\u8de8\u8fc7\uff0c\u4e5f\u53ef\u80fd\u56e0\u4e3a\u8fd9\u4e2a\u6837\u672c\u5728\u65ad\u70b9\u9644\u8fd1\u6ca1\u6709\u53ef\u7528\u7684\u8bfb\u6bb5\u3002\u76f4\u63a5\u5408\u5e76\u5404\u6837\u672c\u7684\u6587\u672c\u884c\uff0c\u53ea\u80fd\u77e5\u9053\u522b\u5904\u6709\u4eba\u62a5\u51fa\u4e86\u8fd9\u4e2a\u4f4d\u7f6e\uff0c\u65e0\u6cd5\u8865\u56de\u539f\u5148\u6587\u4ef6\u7701\u7565\u7684\u5c40\u90e8\u8986\u76d6\u60c5\u51b5\u3002<\/p>\n

Sniffles2 \u5728\u5355\u6837\u672c\u53d1\u73b0\u65f6\u53ef\u4ee5\u53e6\u5916\u5199\u4e00\u4e2a SNF \u6587\u4ef6\uff0c\u4f9b\u8054\u5408\u5206\u6790\u8bfb\u53d6\u5019\u9009\u548c\u8986\u76d6\u7b49\u4fe1\u606f\u3002\u8ba1\u5212\u505a\u961f\u5217\u65f6\uff0c\u7b2c\u4e00\u6b21\u8c03\u7528\u5c31\u540c\u65f6\u4fdd\u5b58\u8fd9\u4e2a\u6587\u4ef6\u548c\u5e38\u89c4\u53d8\u5f02\u8868\u3002\u5bf9\u7167\u8981\u4f7f\u7528\u540c\u4e00\u53c2\u8003\u7248\u672c\u3001\u76f8\u5bb9\u7684\u67d3\u8272\u4f53\u547d\u540d\u4e0e\u6837\u672c\u7f16\u53f7\u3002\u82e5\u53ea\u7559\u4e0b\u4e00\u4e2a\u7ecf\u7b5b\u9009\u7684\u53d8\u5f02\u8868\uff0c\u5230\u8865\u6837\u672c\u65f6\u624d\u53d1\u73b0\u6ca1\u6709\u8be5\u4f4d\u7f6e\u7684\u80cc\u666f\u8bc1\u636e\uff0c\u5373\u4f7f\u628a\u5750\u6807\u5b8c\u5168\u5bf9\u9f50\uff0c\u4e5f\u6ca1\u6cd5\u51ed\u7a7a\u5224\u65ad\u8c01\u80fd\u53ef\u9760\u5206\u578b\u3002\u4f5c\u8005\u7684\u591a\u6837\u672c\u6a21\u5f0f\u4e0e\u8f93\u5165\u8bf4\u660e<\/a><\/p>\n

\u5b9e\u8dd1\u7ecf\u9a8c\uff5c\u53ea\u8ba9\u4e00\u4e2a\u6837\u672c\u5728\u65ad\u70b9\u5904\u6ca1\u6709\u8bfb\u6bb5<\/h2>\n

\u5b9e\u9a8c\u7528\u5341\u4e8c\u4e07\u78b1\u57fa\u7684\u4eba\u5de5\u53c2\u8003\u3002\u5728\u643a\u5e26\u8005\u4e2d\u9020\u51fa\u4e8c\u5341\u56db\u6761\u8de8\u8fc7\u76ee\u6807\u4f4d\u7f6e\u7684\u9ad8\u8d28\u91cf\u6bd4\u5bf9\uff0c\u5341\u4e8c\u6761\u5e26\u76f8\u540c\u7684\u4e09\u767e\u516d\u5341\u78b1\u57fa\u7f3a\u5931\uff0c\u53e6\u5916\u5341\u4e8c\u6761\u4fdd\u7559\u53c2\u8003\u5e8f\u5217\u3002\u7b2c\u4e8c\u4e2a\u6837\u672c\u540c\u6837\u7ed9\u4e8c\u5341\u56db\u6761\u8de8\u8d8a\u8bfb\u6bb5\uff0c\u5168\u90e8\u4e3a\u53c2\u8003\u578b\u3002\u7b2c\u4e09\u4e2a\u6837\u672c\u53ea\u5728\u67d3\u8272\u4f53\u53e6\u4e00\u6bb5\u653e\u5165\u8bfb\u6bb5\uff0c\u76ee\u6807\u5904\u7684\u8de8\u8d8a\u6570\u4e3a\u96f6\u3002\u4e09\u4e2a\u6837\u672c\u5728\u8fdc\u5904\u90fd\u6709\u8bfb\u6bb5\uff0c\u56e0\u800c\u6700\u540e\u4e00\u4e2a\u6837\u672c\u4f9d\u7136\u662f\u4e00\u4efd\u53ef\u6b63\u5e38\u8bfb\u53d6\u548c\u7d22\u5f15\u7684\u6bd4\u5bf9\u6587\u4ef6\u3002\u5b9e\u9645\u8fd0\u884c\u7248\u672c\u4e3a 2.2\uff0c\u5355\u6837\u672c\u6700\u5c11\u652f\u6301\u8bfb\u6bb5\u6570\u660e\u786e\u8bbe\u4e3a\u56db\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u6837\u672c<\/th>\n\u8de8\u8fc7\u5b8c\u6574\u65ad\u70b9\u533a\u7684\u8bfb\u6bb5<\/th>\n\u5355\u6837\u672c\u7f3a\u5931\u8bb0\u5f55<\/th>\n\u8054\u5408 GT<\/th>\n\u8054\u5408 DR \/ DV<\/th>\n<\/tr>\n<\/thead>\n
\u643a\u5e26\u8005<\/td>\n24<\/td>\n1<\/td>\n0\/1<\/td>\n12 \/ 12<\/td>\n<\/tr>\n
\u6709\u53c2\u8003\u652f\u6301<\/td>\n24<\/td>\n0<\/td>\n0\/0<\/td>\n24 \/ 0<\/td>\n<\/tr>\n
\u76ee\u6807\u533a\u6ca1\u6709\u8986\u76d6<\/td>\n0<\/td>\n0<\/td>\n.\/.<\/td>\n0 \/ 0<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

\u56db\u6b21\u8c03\u7528\u4ea7\u751f\u4e00\u6761\u961f\u5217\u4e8b\u4ef6\uff0c\u7c7b\u578b\u4e3a\u7f3a\u5931\uff0c\u957f\u5ea6\u680f\u4e3a\u8d1f\u4e09\u767e\u516d\u5341\u3002\u643a\u5e26\u8005\u7684\u57fa\u56e0\u578b\u8d28\u91cf\u4e3a\u516d\u5341\uff0c\u53e6\u5916\u4e24\u4eba\u7684\u8d28\u91cf\u680f\u5728\u8fd9\u4e2a\u7248\u672c\u7684\u8054\u5408\u8f93\u51fa\u91cc\u90fd\u662f\u96f6\u3002\u7531\u6b64\u53ef\u89c1\uff0c\u5728\u8fd9\u4efd\u8f93\u51fa\u4e0a\u5355\u770b\u8d28\u91cf\u680f\uff0c\u6070\u597d\u5206\u4e0d\u5f00\u6709\u53c2\u8003\u652f\u6301\u548c\u6ca1\u6709\u8986\u76d6\u7684\u6837\u672c\u3002\u8bfb\u8fd9\u4e00\u884c\u8981\u628a\u57fa\u56e0\u578b\u3001\u4e24\u7c7b\u652f\u6301\u8bfb\u6bb5\u4ee5\u53ca\u5c40\u90e8\u8986\u76d6\u653e\u5230\u4e00\u8d77\u3002\u672c\u4f8b\u7528\u4eba\u5de5\u5b89\u6392\u7684\u65e0\u566a\u58f0\u6bd4\u5bf9\uff0c\u4f7f\u53c2\u8003\u652f\u6301\u680f\u6070\u597d\u543b\u5408\u624b\u5de5\u8ba1\u6570\u3002\u771f\u5b9e\u8054\u5408\u7ed3\u679c\u4e2d\u6709\u4e9b\u53c2\u8003\u652f\u6301\u6765\u81ea\u8986\u76d6\u4f30\u8ba1\uff0c\u4e0d\u80fd\u628a\u6bcf\u4e2a\u6570\u90fd\u89e3\u4f5c\u9010\u6761\u4eba\u5de5\u67e5\u770b\u8fc7\u7684\u72ec\u7acb\u5206\u5b50\u3002<\/p>\n

\"\u5355\u6837\u672c\u7a7a\u767d\u7684\u4e24\u79cd\u7ed3\u679c\u3002\u4e09\u4e2a\u6837\u672c\uff0c\u540c\u4e00\u5904
\u4e09\u4e2a\u6837\u672c\uff0c\u540c\u4e00\u5904 360 bp \u7f3a\u5931\uff0c\u8054\u5408\u62a5\u544a\u7ed9\u51fa\u4e09\u79cd\u57fa\u56e0\u578b\u3002<\/figcaption><\/figure>\n

\u591a\u7b97\u4e00\u4e2a\u8fdb\u5165\u5206\u6bcd\u7684\u4eba\uff0c\u9891\u7387\u4f1a\u53d8\u591a\u5c11<\/h2>\n

\u672c\u4f8b\u6309\u4e8c\u500d\u4f53\u5e38\u67d3\u8272\u4f53\u8ba1\u7b97\u3002\u4e24\u4e2a\u6709\u57fa\u56e0\u578b\u7684\u6837\u672c\u5408\u8ba1\u63d0\u4f9b\u56db\u4e2a\u53ef\u4ee5\u8ba1\u6570\u7684\u7b49\u4f4d\uff0c\u5176\u4e2d\u4e00\u4e2a\u4e3a\u7f3a\u5931\uff0c\u793a\u4f8b\u7b49\u4f4d\u9891\u7387\u662f\u56db\u5206\u4e4b\u4e00\u3002\u5982\u679c\u628a\u7b2c\u4e09\u4e2a\u6837\u672c\u7684\u7f3a\u5931\u57fa\u56e0\u578b\u8865\u4e3a\u53c2\u8003\uff0c\u5206\u6bcd\u4f1a\u53d8\u4e3a\u516d\uff0c\u9891\u7387\u4e5f\u4f1a\u53d8\u6210\u516d\u5206\u4e4b\u4e00\u3002\u82e5\u6539\u4e3a\u62a5\u544a\u643a\u5e26\u8005\u6bd4\u4f8b\uff0c\u5e94\u5199\u4e24\u4e2a\u53ef\u5224\u5b9a\u4e2a\u4f53\u4e2d\u4e00\u4eba\u643a\u5e26\uff0c\u5e76\u6ce8\u660e\u5171\u5206\u6790\u4e09\u4eba\u3002\u7ed9\u9891\u7387\u540c\u65f6\u5199\u4e0a\u5206\u5b50\u3001\u53ef\u8c03\u7528\u7684\u5206\u6bcd\u548c\u7f3a\u5931\u6570\uff0c\u8bfb\u8005\u53ef\u4ee5\u5feb\u901f\u53d1\u73b0\u8fd9\u51e0\u79cd\u7edf\u8ba1\u53e3\u5f84\u662f\u5426\u88ab\u6df7\u7528\u4e86\u3002<\/p>\n

# \u4e09\u4e2a BAM \u5747\u5df2\u6309\u5750\u6807\u6392\u5e8f\u5e76\u5efa\u7acb\u7d22\u5f15\uff0c\u4f7f\u7528\u76f8\u540c\u53c2\u8003\r\nfor s in carrier reference gap; do\r\n  sniffles --input "$s.bam" --sample-id "$s" --reference ref.fa \\\r\n    --vcf "$s.vcf" --snf "$s.snf" --minsupport 4 --threads 1\r\ndone\r\nsniffles --input carrier.snf reference.snf gap.snf --vcf cohort.vcf --threads 1\r\nbcftools query -f '%CHROM\\t%POS\\t%INFO\/SVLEN[\\t%GT:%DR:%DV]\\n' cohort.vcf\r\n<\/code><\/pre>\n
\u9047\u5230\u771f\u5b9e\u6837\u672c\u7684\u7a7a\u767d\uff0c\u5148\u4ece\u8054\u5408\u8bb0\u5f55\u63d0\u53d6\u65ad\u70b9\u548c\u4e8b\u4ef6\u957f\u5ea6\uff0c\u518d\u6253\u5f00\u4e24\u4fa7\u6bd4\u5bf9\uff0c\u5206\u522b\u770b\u8bfb\u6bb5\u662f\u5426\u951a\u5b9a\u5230\u552f\u4e00\u4f4d\u7f6e\u3001\u662f\u5426\u6709\u4eba\u4ece\u4e24\u7aef\u8de8\u8fc7\u3001\u7f3a\u5931\u8bfb\u6bb5\u7684\u8d77\u6b62\u70b9\u662f\u5426\u805a\u5728\u540c\u4e00\u6bb5\u3002\u7279\u522b\u957f\u7684\u7f3a\u5931\u548c\u77ed\u7f3a\u5931\u4ea7\u751f\u7684\u8868\u73b0\u4e0d\u540c\uff0c\u6709\u7684\u8bc1\u636e\u5199\u5728\u4e00\u6761\u8bfb\u6bb5\u7684\u6bd4\u5bf9\u64cd\u4f5c\u4e32\u91cc\uff0c\u6709\u7684\u5206\u5e03\u5728\u8865\u5145\u6bd4\u5bf9\u4e2d\u3002\u53ea\u5728\u4e00\u4e2a\u65ad\u70b9\u6570\u6240\u6709\u91cd\u53e0\u8bfb\u6bb5\uff0c\u53ef\u80fd\u628a\u53ea\u5728\u4e00\u4fa7\u505c\u4e0b\u7684\u5206\u5b50\u4e5f\u7b97\u4f5c\u8de8\u8d8a\u652f\u6301\u3002\u6587\u7ae0\u8868\u4e2d\u7684\u8de8\u8d8a\u6570\uff0c\u662f\u5728\u5df2\u77e5\u771f\u503c\u4e0a\u72ec\u7acb\u68c0\u67e5\u8d8a\u8fc7\u4e24\u4e2a\u8fb9\u754c\u7684\u4eba\u5de5\u8bfb\u6bb5\u5f97\u5230\u7684\u3002<\/p>\n
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\u6269\u5230\u961f\u5217\u524d\u7684\u6838\u5bf9\u987a\u5e8f<\/h2>\n
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