可以使用工具 bcftools 中的 view 命令结合选项 -r 和 -s 来挑选特定的 SNP 位点。 选择感兴趣的样本,使用 -s 选项,比如选取样本 A、B、C: bcftools view -s A,B,C input.vcf.gz -o output.vcf.gz 选择特定的区域,使用 -r 选项,比如选择染色体 1 上的某一区域: bcftools view -r 1:100000-20000...
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...
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,可按如下建立索引: bcftools ...
bcftools annotate -x ID,INFO/DP,FORMAT/DP view.vcf -o removed.id.vcf # -x参数表示去除VCF文件中的注释信息,可以是其中的某一列,比如ID, 也可以是某些字段,比如INFO/DP,多个字段的信息用逗号分隔;去除之后,这些信息所在的列并不会去除,而是用.填充。 --rename-chrsfile:旧名字 新名字 空格分隔,一行一...
-r STR only output reads in read group STR [null] -s FLOAT fraction of templates to subsample; integer part as seed [-1] -? longer help 例子: 将sam文件转换成bam文件 $ samtools view -bS abc.sam > abc.bam $ samtools view -b -S abc.sam -o abc.bam ...
(Note that files with non-standard index names can be accessed as e.g. "`bcftools view -r X:2928329 file.vcf.gz##idx##non-standard-index-name`".) BCFtools is designed to work on a stream. It regards an input file "-" as the standard input (stdin) and outputs to the standard ...
header: bcftools view -H *printing variants on a particular region: bcftools view -r chr20:1-200000...by: ~/bin/bcftools/bcftools query -f '[%GT]\n' ../0002.vcf |wc -l #the GT in this case / *selecting...snps from file: ~/bin/bcftools/bcftools view -v snps lc_bams.bcftool...
view命令的主要功能是查看bam和sam文件的内容。 bam文件是sam文件的二进制格式,占用空间小,运算速度快。 view命令的用法和常用参数: Usage: samtools view [options] <in.bam>|<in.sam> [region [...]] 默认情况下不加region,则是输出所有的region. ...
header: bcftools view -H *printing variants on a particular region: bcftools view -r chr20:1-200000...by: ~/bin/bcftools/bcftools query -f '[%GT]\n' ../0002.vcf |wc -l #the GT in this case / *selecting...snps from file: ~/bin/bcftools/bcftools view -v snps lc_bams.bcftool...
add_argument("-l", "--location", dest="location", default="", help="Location for bcftools view (e.g. chr1)") parser.add_argument("-R", "--restrict-regions", dest="regions_bedfile", default=None, type=str, help="Restrict analysis to given (sparse) regions (using -R in ...