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=<...
BCFtools 是一款多种实用工具的集合,它可以用于处理VCF文件和二进制的BCF文件。它可以接受VCF格式、压缩的VCF格式以及BCF格式,并能自动检测输入的格式类型。在有索引文件存在的条件下,BCFtools 可以应用于所有场景,在没有索引文件存在时,BCFtools只能应用于部分场景。通常,在同时读取多个VCFs时,必须对它们建立索引和压缩...
bcftools concat SNP_filtered_sorted.vcf.gzINDEL_filtered_sorted.vcf.gz-a-O z-o ALL_filtered_sorted.vcf.gz 6. 提取指定染色体上的位点: bcftools filter-t chr1,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr2,chr20,chr21,chr22,chr3,chr4,chr5,chr6,chr7,chr8,chr9...
stats .. produce VCF/BCF stats (former vcfcheck) view .. subset, filter and convert VCF and BCF files (1)可从VCF中提取指定样本信息 bcftools index *vcf.gz bcftools view -S samples *vcf.gz -Oz -o *_sampels.vcf.gz (2)对vcf进行过滤 bcftools view -i 'F_MISSING < 15 & MAC > 3' ...
其次分块处理时,即使将example.chr22.impute2的分块内容和example.chr22.impute2_info的分块进行匹配起来,同时example.chr22.impute2_info的分块每一块添加title。即使这样操作程序还报错。因此采用下面的方式进行处理: (2)将gens文件转化为vcf文件 ## 生成的文件格式为:test_vcf.gzfcgene --gens test.impute2...
total number. All filter options, such as ‘-f’, ‘-F’ and ‘-q’ , are taken into account. -1 fast compression (force -b) -x output FLAG in HEX (samtools-C specific) -X output FLAG in string (samtools-C specific) -c print only the count of matching records ...
*bcftools filter *Filter variants per region (in this example, print out only variants mapped to chr1 and chr2) bcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz *printing out info for only 2 samples: ...
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html - bcftools/filter.c at 68c8aba410169e83440b224ab0ed5c82d3d7a6da · samtools/bcftoo
没用过这个命令，你查查bcftools的帮助吧
[W::vcf_parse] FILTER 'SB1' is not defined in the header [W::vcf_parse] FILTER 'DETP20' is not defined in the header [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'SOMATIC' is not defined in the header, assuming Type=...