I used tabix to bgzip them both, but it gives me the message:Failed to open newfile.vcf.gz: not compressed with bgzip Failed to open -: unknown file type I can open the file on its own, and I've played around with the script, but nothing seems to be able to fix this issue. ...
1、bcftools提取指定区段的vcf文件 下载安装bcftools 见如下命令: 1 bcftools filter 1000Genomes.vcf.gz --regions 9:4700000-4800000 > 4700000-4800000.vcf 注意:输入的vcf以gz格式存在,不然会报错:Failed to open 1000Genomes.vcf: not compressed with bgzip 如何将vcf生成gz格式,见这篇文章bcftools将vcf生成b...
使用bcftools压缩vcf文件;如不压缩将会报错 not compressed with bgzip bcftools view file.vcf -Oz -o file.vcf.gz 创建索引 bcftools index file.vcf.gz 提取材料A中特异位点 bcftools isec -C A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz -Oz -o A.unique.vcf.gz 参数含义 -C,--complement 输出只存在...
利用bcftools软件将vcf格式生成gz格式和index格式,需要用到“-Oz”和“index”命令,具体如下: /bcftools-1.8/bin/bcftools view ExAC.vcf -Oz -o ExAC.vcf.gz/bcftools-1.8/bin/bcftools index ExAC.vcf.gz
--include EXPR Include sites and samples for which the expression is true ## --no-version Do not append version and command line to the header ## -o, --output FILE Output file name [stdout] ## -O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VC...
快速提取tab分割文件信息 | 针对GFF、BED和VCF文件,可以使用tabix软件进行快速提取某染色体和某染色体区间的信息。 以VCF文件为例 1.压缩文件 bgzip -f test.vcf 2.建索引 tabix -p vcf test.vcf 3.提取指定区间snp信息 tabix test.vcf.gz 31:19000-20000 ...
bcftools将vcf生成bgzip和index格式 2018-06-07 17:05 − ... 橙子牛奶糖 0 10759 相关推荐 eq(index|-index) 2019-12-09 14:38 − eq(index|-index) 概述 获取当前链式操作中第N个jQuery对象,返回jQuery对象,当参数大于等于0时为正向选取,比如0代表第一个,1代表第二个。当参数为负数时为反向选取...
// check for truncated files, allow only with -f BGZF *fp = bgzf_open(fname, "r"); if ( !fp ) error("index: failed to open %s\n", fname); if ( bgzf_compression(fp)!=2 ) error("index: the file is not BGZF compressed, cannot index: %s\n", fname); if ( bgzf_...
filename # Prepare the opener if the SAM file is compressed if filename.endswith(".gz"): opener = gzip.open else: opener = open min_samples_locus = args.min_samples_locus outgroup = args.outgroup phylipdisable = args.phylipdisable ...
Create tabix index for bgzipped VCF filebgzipVcfFile