$ 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...
根据染色体提取vcf中的信息: bcftools view -r chr20,chr21,chr22 NA12878.vcf.gz -o NA12878.vcf.chr20_22.gz -O z 解释: 提取金标准变异NA12878.vcf.gz中20、21和22染色体的变异,保存到NA12878.vcf.chr20_22.gz文件中 -O z:表示使用压缩形式保存文件 提取之后的文件作为其它软件输入时经常需要索引,...
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... Any help? Thanks! Anna I noticed something simi...
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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
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...
static void usage(args_t *args) { fprintf(stderr, "\n"); fprintf(stderr, "About: VCF/BCF conversion, view, subset and filter VCF/BCF files.\n"); fprintf(stderr, "Usage: bcftools view [options] <in.vcf.gz> [region1 [...]]\n"); ...
bgzip view.vcf bcftools index view.vcf.gz 运行成功后,会生成索引文件view.vcf.gz.csi。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 ...
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