{"id":888,"date":"2022-12-23T20:55:25","date_gmt":"2022-12-23T12:55:25","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=888"},"modified":"2022-12-25T13:49:43","modified_gmt":"2022-12-25T05:49:43","slug":"%e5%a4%9a%e6%a0%b7%e6%9c%acbam%e6%96%87%e4%bb%b6%e5%90%88%e5%b9%b6%e5%8f%8avcf%e6%96%87%e4%bb%b6%e7%94%9f%e6%88%90","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=888","title":{"rendered":"\u591a\u6837\u672cbam\u6587\u4ef6\u5408\u5e76\u53cavcf\u6587\u4ef6\u751f\u6210"},"content":{"rendered":"<p>\u8fdb\u884c\u7ec6\u83cc\u7fa4\u4f53\u57fa\u56e0\u7ec4\u5206\u6790\u65f6\u9700\u8981\u5c06\u591a\u4e2a\u6837\u672c\u6bd4\u5bf9\u5230\u53c2\u8003\u57fa\u56e0\u7ec4\u751f\u6210vcf\u6587\u4ef6\uff0c\u5e38\u7528\u7684\u8f6f\u4ef6\u6709snippy\uff0csnippy\u7684\u7ed3\u679c\u53ea\u5305\u542bcore snp\uff0c\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u65f6\u5f80\u5f80\u9700\u8981\u66f4\u591a\u7684snp\u4fe1\u606f\u3002<\/p>\n<pre>#\u9996\u5148\u5c06snippy\u7684\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u6240\u6709\u6837\u672c\u7684bam\u6587\u4ef6\u5408\u5e76\uff08\u5c06\u6240\u6709\u6837\u672c\u7684bam\u53cabai\u6587\u4ef6\u590d\u5236\u5230\u4e00\u4e2a\u6587\u4ef6\u5939\uff09\nsamtools merge merge.bam *bam\nsamtools mpileup -gSDf ref.fasta merge.bam &gt; merge.bcf\nbcftools call -vm merge.bcf &gt; merge.vcf\n#\u8fc7\u6ee4indel\uff0c\u4fdd\u7559snp\nvcftools --remove-indels --recode --recode-INFO-all --vcf merge.vcf --stdout &gt; merge.snp.vcf\n#\u8fc7\u6ee4\u638950%\u6837\u672c\u4e2d\u7f3a\u5931\u7684SNP\u4f4d\u70b9\nvcftools --vcf merge.snp.vcf --recode --recode-INFO-all --stdout --max-missing 0.5 &gt; merge.filtered.vcf\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u8fdb\u884c\u7ec6\u83cc\u7fa4\u4f53\u57fa\u56e0\u7ec4\u5206\u6790\u65f6\u9700\u8981\u5c06\u591a\u4e2a\u6837\u672c\u6bd4\u5bf9\u5230\u53c2\u8003\u57fa\u56e0\u7ec4\u751f\u6210vcf\u6587\u4ef6\uff0c\u5e38\u7528\u7684\u8f6f\u4ef6\u6709snippy\uff0csnippy\u7684\u7ed3\u679c\u53ea\u5305\u542bcore snp\uff0c\u8fdb\u884c\u4e0b\u6e38\u5206\u6790\u65f6\u5f80\u5f80\u9700\u8981\u66f4\u591a\u7684snp\u4fe1\u606f\u3002 #\u9996\u5148\u5c06snippy\u7684\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u6240\u6709\u6837\u672c\u7684bam\u6587\u4ef6\u5408\u5e76\uff08\u5c06\u6240\u6709\u6837\u672c\u7684bam\u53cabai\u6587\u4ef6\u590d\u5236\u5230\u4e00\u4e2a\u6587\u4ef6\u5939\uff09 samtools merge merge.bam *bam samtools mpileup -gSDf ref.fasta merge.bam &gt; merge.bcf bcftools call -vm merge.bcf &gt; merge.vcf #\u8fc7\u6ee4indel\uff0c\u4fdd\u7559snp vcftools &#8211;remove-indels &#8211;recode &#8211;recode-INFO-all &#8211;vcf merge.vcf &#8211;stdout &gt; merge.snp.vcf #\u8fc7\u6ee4\u638950%\u6837\u672c\u4e2d\u7f3a\u5931\u7684SNP\u4f4d\u70b9 vcftools &#8211;vcf merge.snp.vcf &#8211;recode &#8211;recode-INFO-all &#8211;stdout &#8211;max-missing 0.5 &gt; merge.filtered.vcf<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/888"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=888"}],"version-history":[{"count":2,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/888\/revisions"}],"predecessor-version":[{"id":890,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/888\/revisions\/890"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=888"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=888"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=888"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}