$ 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 view abc.bam scaffold1:30000-100000 $gt; scaffold1_30k-100k.sam 根据fasta文件,将 header 加入到 sam 或 bam 文件中 $ samtools view -T genome.fasta -h scaffold1.sam > scaffold1.h...
#有了索引文件后,可以使用以下命令很快从基因组中提取到fasta格式的子序列$ samtools faidx genome.fa chr1>chr1.fa 6. tview tview能直观的显示出reads比对到基因组的情况,和基因组浏览器有点类似。 Usage: samtools tview <aln.bam> [ref.fasta] 当给出参考基因组的时候,会在第一排显示参考基因组的序列...
如果需要建立.tbi 格式的索引,用法如下 bcftools index -t view.vcf.gz tbi 索引文件为 view.vcf.gz.tbi。 2. view view 命令可以用于 VCF 和 BCF 格式的转换,用法如下 bcftools view view.vcf.gz -O u -o view.bcf -O 参数指定输出文件的类型,b 代表压缩后的 BCF 文件,u 代表 未经压缩的 BCF 文件...
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bcftools view -cNegv samtools_result.bcf > samtools_result.vcf 命令解释：veiw 是bcftools中主要的方法，‘Convert between BCF and VCF ， call variant candidates and estimate allele frequencies.’-c Call variants using Bayesian inference .-N Skip sites where the REF field is not A/T...
Hi, I am using bcftools view -R regions.bed input.vcf.gz to extract only those variants present in regions.bed. However, I get only those variants not present in regions.bed, so exactly the opposite. I really don't know what is going on...
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$ bwa mem –t 40 ref.fa read1.fq read2.fq >aln-pe.sam 二、转换 $ samtools view -bS aln-pe.sam > aln-pe.bam $ samtools sort -@ 40 aln-6.bam > aln-6.sorted.bam $ samtools sort –o aln-pe-sorted.bam aln-pe.bam
$ 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...
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