{"id":25556,"date":"2024-01-22T17:02:27","date_gmt":"2024-01-22T09:02:27","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25556"},"modified":"2024-01-22T17:02:28","modified_gmt":"2024-01-22T09:02:28","slug":"%e4%b8%a4%e5%88%86%e9%92%9f%e6%95%99%e4%bd%a0%e5%ae%8c%e6%88%90%e5%8f%98%e5%bc%82%e6%a3%80%e6%b5%8b","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=25556","title":{"rendered":"\u4e24\u5206\u949f\u6559\u4f60\u5b8c\u6210\u53d8\u5f02\u68c0\u6d4b"},"content":{"rendered":"
\u5728\u524d\u9762\u7684\u6559\u7a0b\u4e2d\uff0c\u5c0f\u679c\u5df2\u7ecf\u7ed9\u5927\u5bb6\u5206\u4eab\u4e86\u8d28\u91cf\u8bc4\u4f30\u3001\u5e8f\u5217\u6bd4\u5bf9\u7b49\u64cd\u4f5c\uff0c\u76f8\u4fe1\u5c0f\u4f19\u4f34\u4eec\u4e5f\u662f\u6536\u83b7\u6ee1\u6ee1\u3002\u90a3\u4e48\u4eca\u5929\uff0c\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u8fc8\u5165\u65b0\u7684\u9636\u6bb5\uff0c\u63ed\u5f00\u53d8\u5f02\u68c0\u6d4b\u7684\u795e\u79d8\u9762\u7eb1~\u50cf\u5f80\u5e38\u4e00\u6837\u5c0f\u679c\u5949\u884c\u7740\u201c\u5148\u8dd1\u6d41\u7a0b\uff0c\u540e\u770b\u539f\u7406\u201d\u7684\u6d41\u7a0b\uff0c\u8fd9\u4e00\u6b21\u5148\u7ed9\u5927\u5bb6\u8be6\u7ec6\u5730\u4ecb\u7ecd\u53d8\u5f02\u68c0\u6d4b\u7684\u5168\u90e8\u6d41\u7a0b\uff0c\u4e0b\u4e00\u6b21\u518d\u7ed9\u5927\u5bb6\u5206\u4eab\u53d8\u5f02\u68c0\u6d4b\u7684\u539f\u7406\u3002\u597d\u5566\uff0c\u5e9f\u8bdd\u4e0d\u591a\u8bf4\uff0c\u6211\u4eec\u76f4\u63a5\u5f00\u59cb~<\/h6>\n

\u64cd\u4f5c\u4ee3\u7801<\/h2>\n

\u50cf\u4e4b\u524d\u4e00\u6837\uff0c\u5c0f\u679c\u5f00\u95e8\u89c1\u5c71\u5148\u628a\u64cd\u4f5c\u6240\u9700\u8981\u7684\u5168\u90e8\u4ee3\u7801\u5148\u63d0\u4f9b\u7ed9\u5927\u5bb6\uff0c\u5e2e\u52a9\u6025\u9700\u64cd\u4f5c\u7684\u5c0f\u4f19\u4f34\u4eec\u89e3\u71c3\u7709\u4e4b\u6025\uff1a<\/p>\n

# \u521b\u5efa\u7d22\u5f15
\nsamtools index .\/02_align\/test.clean.sort.uniq.bam
\n# \u9009\u7528freebayes\u8fdb\u884c\u53d8\u5f02\u68c0\u6d4b
\nfreebayes -m 30 -q 20 -f .\/00_ref\/MGI358.SNP.fa -@ .\/00_ref\/alleles_all.vcf.gz -t .\/00_ref\/target.358.SE50.subSNP.bed –report-all-haplotype-alleles .\/02_align\/test.clean.sort.uniq.bam > .\/03_SNPCalling\/test.clean.SNP.vcf
\n# \u5c06vcf\u6587\u4ef6\u7684\u8def\u5f84\u5199\u5165vcf.list\u6587\u4ef6
\necho “test .\/03_SNPCalling\/test.clean.SNP.vcf 1” > .\/03_SNPCalling\/vcf.list
\n# \u4f7f\u7528vcf2geno_free.pl\u8fdb\u884c\u57fa\u56e0\u578b\u8f6c\u6362
\nperl vcf2geno_free.pl -in .\/03_SNPCalling\/vcf.list -dir .\/03_SNPCalling\/ -std
\n.\/00_ref\/alleles_all.vcf.gz -summary<\/p>\n

\u4ee5\u4e0a\u5c31\u662f\u53d8\u5f02\u68c0\u6d4b\u6240\u9700\u8981\u7684\u5168\u90e8\u4ee3\u7801\u5566\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u5462~\u5982\u679c\u5c0f\u4f19\u4f34\u4eec\u5e73\u65f6\u5728\u751f\u4fe1\u5206\u6790\u7684\u64cd\u4f5c\u8fc7\u7a0b\u4e2d\u9047\u5230\u56f0\u96be\uff0c\u4e5f\u6b22\u8fce\u5927\u5bb6\u4f7f\u7528\u5c0f\u679c\u5f00\u53d1\u7684\u751f\u4fe1\u5de5\u5177\u5e73\u53f0http:\/\/www.biocloudservice.com\/home.html<\/a>\u54e6~<\/p>\n

\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u4f1a\u7ed9\u5927\u5bb6\u8be6\u7ec6\u5730\u4ecb\u7ecd\u7528\u5230\u7684\u5de5\u5177\u548c\u6bcf\u4e00\u6b65\u4ee3\u7801\u7684\u53c2\u6570\u4ee5\u53ca\u5bf9\u7ed3\u679c\u8fdb\u884c\u5206\u6790\uff0c\u5c0f\u4f19\u4f34\u4eec\u5343\u4e07\u4e0d\u8981\u8d70\u5f00\u54e6~<\/p>\n

\u5de5\u5177\u4ecb\u7ecd<\/h2>\n

FreeBayes<\/h3>\n

\u4ecb\u7ecd<\/h4>\n

FreeBayes\u662f\u4e00\u4e2a\u7528\u4e8e\u57fa\u56e0\u7ec4\u53d8\u5f02\u68c0\u6d4b\u548c\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff08Single Nucleotide Polymorphism\uff0cSNP\uff09\u5206\u6790\u7684\u5f00\u6e90\u8f6f\u4ef6\u5de5\u5177\uff0c\u5b83\u80fd\u591f\u4ece\u4e0b\u4e00\u4ee3\u6d4b\u5e8f\u6570\u636e\u4e2d\u51c6\u786e\u5730\u9274\u5b9a\u51faSNP\u3001\u5c0f\u7247\u6bb5\u63d2\u5165\/\u5220\u9664\uff08indel\uff09\u548c\u7ed3\u6784\u53d8\u5f02\u7b49\u57fa\u56e0\u7ec4\u53d8\u5f02\u3002<\/p>\n

FreeBayes\u7684\u5de5\u4f5c\u539f\u7406\u57fa\u4e8e\u8d1d\u53f6\u65af\u5b9a\u7406\u548c\u5355\u6837\u672c\u6bd4\u5bf9\u3002\u5b83\u5229\u7528\u5df2\u6bd4\u5bf9\u7684\u6d4b\u5e8f\u6570\u636e\u548c\u53c2\u8003\u57fa\u56e0\u7ec4\u6765\u8ba1\u7b97\u6bcf\u4e2a\u4f4d\u70b9\u4e0a\u7684\u53d8\u5f02\u6982\u7387\uff0c\u5e76\u901a\u8fc7\u7edf\u8ba1\u6a21\u578b\u5bf9\u7a81\u53d8\u8fdb\u884c\u7b5b\u9009\u548c\u8fc7\u6ee4\u3002\u4e0e\u5176\u4ed6\u5e38\u89c1\u7684SNP\u9274\u5b9a\u5de5\u5177\u76f8\u6bd4\uff0cFreeBayes\u5728\u5904\u7406\u9ad8\u6742\u5408\u5ea6\u548c\u590d\u6742\u53d8\u5f02\u7684\u60c5\u51b5\u4e0b\u8868\u73b0\u8f83\u597d\u3002<\/p>\n

FreeBayes\u5177\u6709\u4ee5\u4e0b\u7279\u70b9\uff1a<\/p>\n

    \n
  1. \u9ad8\u7075\u654f\u5ea6\uff1aFreeBayes\u5728\u9274\u5b9a\u4f4e\u9891\u7387\u53d8\u5f02\uff08\u5982\u7a81\u53d8\u7b49\uff09\u65b9\u9762\u8868\u73b0\u4f18\u79c0\uff0c\u80fd\u591f\u51c6\u786e\u5730\u8bc6\u522b\u51fa\u8f83\u7f55\u89c1\u7684\u53d8\u5f02\u3002<\/li>\n
  2. \u591a\u6837\u6027\u652f\u6301\uff1aFreeBayes\u53ef\u4ee5\u5728\u4e0d\u540c\u7c7b\u578b\u7684\u6837\u672c\uff08\u5982\u4eba\u7c7b\u3001\u52a8\u690d\u7269\u7b49\uff09\u4e0a\u4f7f\u7528\uff0c\u5e76\u4e14\u9002\u7528\u4e8e\u4e0d\u540c\u79cd\u7c7b\u7684\u6d4b\u5e8f\u6570\u636e\uff08\u5982Illumina\u3001PacBio\u3001ONT\u7b49\uff09\u3002<\/li>\n
  3. \u533a\u57df\u611f\u77e5\uff1aFreeBayes\u53ef\u4ee5\u9488\u5bf9\u7279\u5b9a\u611f\u5174\u8da3\u533a\u57df\u8fdb\u884c\u53d8\u5f02\u68c0\u6d4b\uff0c\u4ece\u800c\u63d0\u9ad8\u5206\u6790\u7684\u6548\u7387\u548c\u51c6\u786e\u6027\u3002<\/li>\n
  4. \u5e76\u884c\u5904\u7406\uff1aFreeBayes\u652f\u6301\u5e76\u884c\u8ba1\u7b97\uff0c\u53ef\u4ee5\u5229\u7528\u591a\u4e2a\u5904\u7406\u5668\u6216\u8ba1\u7b97\u8282\u70b9\u8fdb\u884c\u9ad8\u6548\u7684\u53d8\u5f02\u68c0\u6d4b\u3002<\/li>\n
  5. \u5f00\u6e90\u514d\u8d39\uff1aFreeBayes\u662f\u4e00\u4e2a\u5f00\u6e90\u8f6f\u4ef6\uff0c\u7528\u6237\u53ef\u4ee5\u81ea\u7531\u5730\u4f7f\u7528\u3001\u4fee\u6539\u548c\u5206\u53d1\u3002<\/li>\n<\/ol>\n

    \u5355\u500d\u578b\uff08\u5355\u500d\u4f53\u57fa\u56e0\u578b\u7684\u7b80\u79f0\uff09\u5728\u9057\u4f20\u5b66\u4e0a\u662f\u6307\u5728\u540c\u4e00\u67d3\u8272\u4f53\u4e0a\u8fdb\u884c\u5171\u540c\u9057\u4f20\u7684\u591a\u4e2a\u57fa\u56e0\u5ea7\uff08\u5373\u4f4d\u70b9\uff09\u4e0a\u7b49\u4f4d\u57fa\u56e0\u7684\u7ec4\u5408<\/strong>\uff1b\u901a\u4fd7\u7684\u8bf4\u6cd5\u5c31\u662f\u82e5\u5e72\u4e2a\u51b3\u5b9a\u540c\u4e00\u6027\u72b6\u7684\u7d27\u5bc6\u8fde\u9501\u7684\u57fa\u56e0\u6784\u6210\u7684\u57fa\u56e0\u578b\u3002<\/strong> \u6309\u7167\u67d0\u4e00\u6307\u5b9a\u57fa\u56e0\u5ea7\u4e0a\u57fa\u56e0\u91cd\u7ec4\u53d1\u751f\u7684\u6570\u91cf\uff0c\u5355\u500d\u578b\u53ef\u4ee5\u6307\u81f3\u5c11\u4e24\u4e2a\u57fa\u56e0\u5ea7\u751a\u81f3\u6574\u4e2a\u67d3\u8272\u4f53\u3002<\/p>\n

    FreeBayes\u4e5f\u53ef\u4ee5\u79f0\u4e3a\u8d1d\u53f6\u65af\u9057\u4f20\u53d8\u5f02\u68c0\u6d4b\u5668\uff0c\u5176\u4e3b\u8981\u76ee\u6807\u662f\u901a\u8fc7\u5206\u6790\u5355\u500d\u578b\u6765\u5bfb\u627e\u5c0f\u578b\u591a\u6001\u6027\u4e8b\u4ef6\uff08\u4f8b\u5982SNP\uff08\u5355\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\u3001indels\uff08\u63d2\u5165\u548c\u5220\u9664\u4e8b\u4ef6\uff09\u3001MNP\uff08\u591a\u6838\u82f7\u9178\u591a\u6001\u6027\uff09\uff09\u548c\u590d\u6742\u4e8b\u4ef6\uff08\u590d\u5408\u63d2\u5165\u548c\u66ff\u6362\u4e8b\u4ef6\uff09\u3002\u5b83\u901a\u8fc7\u4f7f\u7528\u5e26\u6709\u7f16\u7801\u8d28\u91cf\u5206\u6570\uff08Phred+33\uff0c\u5177\u4f53\u4fe1\u606f\u5c0f\u679c\u5728\u7b2c\u4e00\u671f\u4e2d\u5206\u4eab\u8fc7\uff09\u7684BAM\u6587\u4ef6\u4e2d\u7684reads\u6bd4\u5bf9\u7ed3\u679c\uff0c\u5bf9\u4efb\u610f\u6570\u91cf\u7684\u4e2a\u4f53\u548c\u53c2\u8003\u57fa\u56e0\u7ec4\uff08FASTA\u683c\u5f0f\uff09\u8fdb\u884c\u6bd4\u5bf9\uff0c\u4ece\u800c\u786e\u5b9a\u5728\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u6bcf\u4e2a\u4f4d\u7f6e\u4e0a\u7fa4\u4f53\u6700\u53ef\u80fd\u7684\u57fa\u56e0\u578b\u7ec4\u5408\u3002\u8fd9\u79cd\u65b9\u6cd5\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u4e86\u89e3\u4e0d\u540c\u4e2a\u4f53\u7684\u57fa\u56e0\u7ec4\u5dee\u5f02\uff0c\u5e76\u63ed\u793a\u9057\u4f20\u53d8\u5f02\u4e0e\u75be\u75c5\u7b49\u91cd\u8981\u751f\u7269\u5b66\u73b0\u8c61\u4e4b\u95f4\u7684\u5173\u8054\u3002<\/p>\n

    \u5173\u4e8e\u5c0f\u578b\u591a\u6001\u6027\u4e8b\u4ef6\uff08\u5373\u57fa\u56e0\u7ec4\u4e2d\u7684\u8f83\u5c0f\u89c4\u6a21\u7684\u53d8\u5f02\u60c5\u51b5\uff09\u7684\u66f4\u591a\u8be6\u7ec6\u4fe1\u606f\u5c0f\u679c\u4e5f\u4f1a\u5728\u540e\u9762\u53d8\u5f02\u68c0\u6d4b\u7684\u539f\u7406\u8be6\u89e3\u5206\u4eab\u4e2d\u7ed9\u5927\u5bb6\u5e26\u6765\uff0c\u5c0f\u4f19\u4f34\u4eec\u8bb0\u5f97\u6301\u7eed\u5173\u6ce8\u54e6~<\/p>\n

    \u8c03\u7528\u547d\u4ee4\uff1a<\/p>\n

    freebayes -f ref.fa aln.bam \\>var.vcf<\/p>\n

    \u5e38\u7528\u53c2\u6570<\/h4>\n

    \u5c0f\u679c\u5728\u8fd9\u91cc\u8fd8\u4e3a\u5927\u5bb6\u6574\u7406\u4e86FreeBayes\u5e38\u7528\u7684\u4e00\u4e9b\u53c2\u6570\u53ca\u5176\u529f\u80fd\uff1a<\/p>\n

      \n
    1. –fasta-reference\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u6307\u5b9a\u53c2\u8003\u57fa\u56e0\u7ec4\u7684FASTA\u6587\u4ef6\u3002\u53c2\u8003\u57fa\u56e0\u7ec4\u662f\u8fdb\u884c\u6bd4\u5bf9\u548c\u53d8\u5f02\u68c0\u6d4b\u7684\u57fa\u7840\uff0c\u901a\u8fc7\u6307\u5b9aFASTA\u6587\u4ef6\u53ef\u4ee5\u544a\u77e5FreeBayes\u4f7f\u7528\u54ea\u4e2a\u57fa\u56e0\u7ec4\u4f5c\u4e3a\u53c2\u8003\u8fdb\u884c\u5206\u6790\u3002<\/li>\n
    2. –bam\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u6307\u5b9a\u6bd4\u5bf9\u6d4b\u5e8f\u6570\u636e\u7684BAM\u6587\u4ef6\u3002BAM\u6587\u4ef6\u662f\u5b58\u50a8\u6d4b\u5e8f\u6570\u636e\u6bd4\u5bf9\u7ed3\u679c\u7684\u4e8c\u8fdb\u5236\u683c\u5f0f\u6587\u4ef6\uff0c\u5305\u542b\u4e86\u6bcf\u4e2a\u6d4b\u5e8fRead\u7684\u6bd4\u5bf9\u4f4d\u7f6e\u3001\u8d28\u91cf\u7b49\u4fe1\u606f\u3002\u901a\u8fc7\u6307\u5b9aBAM\u6587\u4ef6\uff0cFreeBayes\u53ef\u4ee5\u4ece\u4e2d\u8bfb\u53d6\u6bd4\u5bf9\u4fe1\u606f\uff0c\u5e76\u8fdb\u884c\u53d8\u5f02\u68c0\u6d4b\u3002<\/li>\n
    3. –min-alternate-count\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u7684\u975e\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u8ba1\u6570\u9608\u503c\u3002\u5728\u5355\u4e2a\u4e2a\u4f53\u4e2d\uff0c\u5982\u679c\u67d0\u4e2a\u4f4d\u7f6e\u7684\u975e\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u7684\u89c2\u5bdf\u6570\u4f4e\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u4f4d\u7f6e\u7684\u7b49\u4f4d\u57fa\u56e0\u5c06\u88ab\u8fc7\u6ee4\u6389\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u5bf9\u4e8e\u53cc\u500d\u4f53\u6837\u672c\uff0c\u8be5\u503c\u4e3a2\u3002<\/li>\n
    4. –min-alternate-fraction\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u7684\u975e\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u9891\u7387\u9608\u503c\u3002\u5982\u679c\u67d0\u4e2a\u4f4d\u7f6e\u7684\u975e\u53c2\u8003\u7b49\u4f4d\u57fa\u56e0\u5728\u4e2a\u4f53\u4e2d\u7684\u9891\u7387\u4f4e\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u4f4d\u7f6e\u7684\u7b49\u4f4d\u57fa\u56e0\u5c06\u88ab\u8fc7\u6ee4\u6389\u3002<\/li>\n
    5. –ploidy\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u6307\u5b9a\u6837\u672c\u7684\u500d\u6027\uff08\u5373\u67d3\u8272\u4f53\u7684\u62f7\u8d1d\u6570\uff09\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0cFreeBayes\u5047\u8bbe\u6837\u672c\u4e3a\u4e8c\u500d\u4f53\uff08diploid\uff09\uff0c\u53ef\u4ee5\u6839\u636e\u5b9e\u9645\u60c5\u51b5\u8fdb\u884c\u4fee\u6539\u3002<\/li>\n
    6. –genotype-qualities\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8ba1\u7b97\u57fa\u56e0\u578b\u7684\u4f3c\u7136\u6bd4\uff0c\u5e76\u5c06\u7ed3\u679c\u8f93\u51fa\u5230VCF\u6587\u4ef6\u4e2d\u3002\u57fa\u56e0\u578b\u8d28\u91cf\u5206\u6570\uff08genotype qualities\uff09\u7528\u4e8e\u8861\u91cf\u57fa\u56e0\u578b\u63a8\u65ad\u7684\u53ef\u9760\u6027\u548c\u51c6\u786e\u6027\u3002<\/li>\n
    7. –min-mapping-quality\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u7684\u6bd4\u5bf9\u8d28\u91cf\u9608\u503c\u3002\u5982\u679c\u67d0\u4e2a\u6bd4\u5bf9\u7684\u8d28\u91cf\u4f4e\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u6bd4\u5bf9\u5c06\u88ab\u8fc7\u6ee4\u6389\u3002\u8fd9\u4e2a\u53c2\u6570\u5728\u53ea\u9700\u8981\u8fdb\u884c\u53d8\u5f02\u68c0\u6d4b\u800c\u4e0d\u9700\u8981\u989d\u5916\u9700\u6c42\u65f6\uff0c\u53ef\u4ee5\u4f7f\u7528\u9ed8\u8ba4\u503c\uff08\u5bf9\u4e8e\u53cc\u500d\u4f53\u751f\u7269\u6765\u8bf4\uff09\u3002<\/li>\n
    8. –min-base-quality\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u7684\u78b1\u57fa\u8d28\u91cf\u9608\u503c\u3002\u5982\u679c\u67d0\u4e2a\u78b1\u57fa\u7684\u8d28\u91cf\u4f4e\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u78b1\u57fa\u5c06\u88ab\u8fc7\u6ee4\u6389\u3002<\/li>\n
    9. –min-supporting-mapping-quality\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u7684\u652f\u6301\u6bd4\u5bf9\u8d28\u91cf\u9608\u503c\u3002\u5982\u679c\u67d0\u4e2a\u6bd4\u5bf9\u7684\u8d28\u91cf\u4f4e\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u6bd4\u5bf9\u5c06\u4e0d\u4f1a\u88ab\u89c6\u4e3a\u652f\u6301\u53d8\u5f02\u3002<\/li>\n
    10. –min-supporting-base-quality\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u7684\u652f\u6301\u78b1\u57fa\u8d28\u91cf\u9608\u503c\u3002\u5982\u679c\u67d0\u4e2a\u78b1\u57fa\u7684\u8d28\u91cf\u4f4e\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u78b1\u57fa\u5c06\u4e0d\u4f1a\u88ab\u89c6\u4e3a\u652f\u6301\u53d8\u5f02\u3002<\/li>\n
    11. –min-indel-support\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u7684\u63d2\u5165\/\u5220\u9664\u7684\u652f\u6301\u9608\u503c\u3002\u5982\u679c\u67d0\u4e2a\u63d2\u5165\u6216\u5220\u9664\u7684\u652f\u6301\u6570\u4f4e\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u63d2\u5165\/\u5220\u9664\u5c06\u88ab\u8fc7\u6ee4\u6389\u3002<\/li>\n
    12. –min-strand-bias-pvalue\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8bbe\u5b9a\u6700\u5c0f\u504f\u5411\u67d0\u4e00\u94fe\u7684\u504f\u501a\u68c0\u9a8cP\u503c\u9608\u503c\u3002\u5982\u679c\u4f4d\u70b9\u7684\u504f\u501a\u68c0\u9a8cP\u503c\u9ad8\u4e8e\u8fd9\u4e2a\u9608\u503c\uff0c\u90a3\u4e48\u8be5\u4f4d\u70b9\u5c06\u88ab\u8fc7\u6ee4\u6389\u3002<\/li>\n
    13. –exclude-unobserved-genotypes\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u6392\u9664\u672a\u89c2\u5bdf\u5230\u7684\u57fa\u56e0\u578b\uff0c\u5373\u5728\u5206\u6790\u7ed3\u679c\u4e2d\u4e0d\u5305\u542b\u672a\u89c2\u5bdf\u5230\u7684\u57fa\u56e0\u578b\u3002<\/li>\n
    14. –genotype-qualities\uff1a\u8be5\u53c2\u6570\u7528\u4e8e\u8ba1\u7b97\u57fa\u56e0\u578b\u7684\u8fb9\u9645\u6982\u7387\uff0c\u5e76\u8f93\u51fa\u5230VCF\u6587\u4ef6\u4e2d\u3002\u57fa\u56e0\u578b\u7684\u8fb9\u9645\u6982\u7387\u662f\u57fa\u4e8e\u89c2\u5bdf\u5230\u7684\u6d4b\u5e8f\u6570\u636e\u548c\u57fa\u56e0\u578b\u8d28\u91cf\u7b49\u4fe1\u606f\u8fdb\u884c\u63a8\u65ad\u7684\u7ed3\u679c\u3002<\/li>\n<\/ol>\n

      \u8fd9\u4e9b\u4ec5\u662fFreeBayes\u53ef\u7528\u53c2\u6570\u4e2d\u7684\u4e00\u90e8\u5206\uff0c\u8fd8\u6709\u5176\u4ed6\u4e00\u4e9b\u9ad8\u7ea7\u53c2\u6570\u548c\u8fc7\u6ee4\u9009\u9879\uff0c\u7528\u4e8e\u66f4\u7cbe\u7ec6\u5730\u63a7\u5236\u53d8\u5f02\u68c0\u6d4b\u8fc7\u7a0b\u3002\u5728\u4f7f\u7528FreeBayes\u65f6\uff0c\u5927\u5bb6\u53ef\u4ee5\u901a\u8fc7\u67e5\u770b\u76f8\u5173\u6587\u6863\u6216\u8fd0\u884c ‘freebayes –help’ \u547d\u4ee4\u83b7\u53d6\u66f4\u8be6\u7ec6\u7684\u53c2\u6570\u8bf4\u660e\u548c\u7528\u6cd5\u793a\u4f8b\u3002<\/p>\n

      vcf2geno_free.pl<\/h3>\n

      vcf2geno_free.pl\u662f\u4e00\u4e2a\u7528\u4e8e\u5c06VCF\u6587\u4ef6\u8f6c\u6362\u4e3a\u57fa\u56e0\u578b\u6587\u4ef6\u7684Perl\u811a\u672c\uff0c\u5b83\u53ef\u4ee5\u5c06VCF\u6587\u4ef6\u4e2d\u7684\u591a\u4e2a\u6837\u672c\u7684\u53d8\u5f02\u4f4d\u70b9\u7684\u57fa\u56e0\u578b\u4fe1\u606f\u63d0\u53d6\u5e76\u8f93\u51fa\u5230\u4e00\u4e2a\u57fa\u56e0\u578b\u6587\u4ef6\u4e2d\uff0c\u65b9\u4fbf\u540e\u7eed\u7684\u9057\u4f20\u5206\u6790\u548c\u7edf\u8ba1\u5206\u6790\u3002<\/p>\n

      \u4f7f\u7528vcf2geno_free.pl\u65f6\uff0c\u9700\u8981\u6307\u5b9a\u8f93\u5165\u7684VCF\u6587\u4ef6\u548c\u8f93\u51fa\u7684\u57fa\u56e0\u578b\u6587\u4ef6\u3002<\/p>\n

      \u4f8b\u5982\uff0c\u4ee5\u4e0b\u547d\u4ee4\u53ef\u4ee5\u5c06input.vcf\u6587\u4ef6\u8f6c\u6362\u4e3aoutput.geno\u6587\u4ef6\uff1a<\/p>\n

      perl vcf2geno_free.pl –input input.vcf –output output.geno<\/p>\n

      \u5c0f\u4f19\u4f34\u4eec\u4f7f\u7528\u4e4b\u524d\u9700\u8981\u786e\u4fdd\u5df2\u7ecf\u5b89\u88c5\u4e86Perl\u73af\u5883\uff0c\u5e76\u4e14\u5b89\u88c5\u4e86\u6240\u9700\u7684\u4f9d\u8d56\u6a21\u5757\u54e6\u3002<\/p>\n

      \u6d41\u7a0b\u8be6\u89e3<\/h2>\n

      \u4e0a\u9762\u7684\u4ee3\u7801\u53ef\u80fd\u6709\u7684\u5c0f\u4f19\u4f34\u4e0d\u662f\u5f88\u7406\u89e3\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u7ed9\u5c0f\u4f19\u4f34\u4eec\u8be6\u7ec6\u5730\u9010\u53e5\u89e3\u91ca\u4e00\u4e0b\uff1a<\/p>\n

      samtools index .\/02_align\/test.clean.sort.uniq.bam<\/p>\n