bcftools view -h sample.vcf##fileformat=VCFv4.2##FILTER=<ID=PASS,Description="All filters passed">##bcftoolsVersion=1.5+htslib-1.5##bcftoolsCommand=mpileup -f /public/analysis/ucsc.hg19.fasta -Ou /public/analysis/result/sample.bam##reference=file:///public/analysis/ucsc.hg19.fasta##contig=<...
$ samtools view -bF 12 abc.bam > abc.F12.bam 提取没有比对到参考序列上的比对结果 $ samtools view -bf 4 abc.bam > abc.f.bam 提取bam文件中比对到caffold1上的比对结果,并保存到sam文件格式 $ samtools view abc.bam scaffold1 > scaffold1.sam 提取scaffold1上能比对到30k到100k区域的比对结果 $...
$samtools mpileup -gUf ./GCF.fa 1.sorted.bam -o 1.bcf #-g,输出格式为BCF;-U ,输出格式不压缩,利于下步分析;-f,faidx后的REF #bcftools call SNP $bcftools view -cvNg 1.bcf>1.vcf#-c,用贝叶斯推理进行calling;-v,只输出variant位点(force -c);-g 在variant位点,call per-sample genotypes(fo...
只需要把两个4+8的值12作为过滤参数即可$ samtools view-b-F12a.bam>a.F12.bam#提取没有比对到参考序列上的比对结果$ samtools view-b-f4a.bam>a.f4.bam#提取bam文件比对到scaffold1上的比对结果,并保存成sam
By company size Enterprises Small and medium teams Startups Nonprofits By use case DevSecOps DevOps CI/CD View all use cases By industry Healthcare Financial services Manufacturing Government View all industries View all solutions Resources Topics AI DevOps Security Software Development...
fprintf(stderr, "Usage: bcftools view [options] <in.vcf.gz> [region1 [...]]\n"); fprintf(stderr, "\n"); fprintf(stderr, "Output options:\n"); fprintf(stderr, " -G, --drop-genotypes drop individual genotype information (after subsetting if -s option set)\n"); fprintf...
-g Compute genotype likelihoods and output them in the binary call format(BCF).-D Output per-sample read depth > 是将结果保存到samtools_result.bcf文件中 最终得到的samtools_result.bcf 是二进制文件，到此完成了call snp的第一步。得到bcf文件以后，第二步执行命令：bcftools view -cNegv ...
Reply to this email directly or view it on GitHub. cpenkett commented Dec 9, 2014 I tried Ernest's pipeline: unnormalise all component files with norm -m +any merge with -m all normalise the merged file with -m -any and I get lines like this: 22 49557389 . A G 413 PASS SNVSB...
$ samtools view -T genome.fasta -h scaffold1.bam > scaffold1.h.sam 2. sort sort用来对bam文件进行排序 Usage: samtools sort [-n] [-m <maxMem>] <in.bam> <out.prefix> Options: -m 设置运行内存大小,默认是500,000,000(即500M,支持K/M/G缩写)。对于处理大数据时,如果内存够用,可设置大些...