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...
## 生成压缩文件的索引为test.recode.vcf.gz.tbibcftools index -t test.recode.vcf.gz## 生成压缩文件的索引为test.recode.vcf.gz.csibcftools index test.recode.vcf.gz 4. fcgene的使用 (1)官方使用说明文档 ./fcgene --gens example/example.chr22.impute2 --thresh0.9\--info example/example.chr22.i...
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' ...
This leads to inconsistent behavior, as shown in the following example:(echo "##fileformat=VCFv4.2" echo "##contig=<ID=chr1>" echo "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">" echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tA\tB" echo -e ...
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 ...
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
zcat ~/data/database/2021Q4/HGMD_Pro_2021.4_hg19.vcf.gz | \ awk ‘/^##contig/ {next} /^#CHROM/ {printf(“##contig= bcftools annotate —rename-chrs /bi/database/chr-names.txt -x ^INFO/CLASS | \ bcftools query -f “%CHROM\t%POS\t%ID\t%REF\t%ALT\t%QUAL\t%FILTER\t%INFO/...
#include <htslib/vcf.h> #include <htslib/synced_bcf_reader.h> #include <htslib/vcfutils.h> #include "bcftools.h" #include "filter.h" #include "rbuf.h" // Logic of the filters: include or exclude sites which match the filters?#...