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...
修改vcf.gz染色体编号方式 nohup bcftools annotate --rename-chrs chr_id.txt xx.vcf.gz -Oz -o xxx.vcf.gz --threads 23 & 统计vcf中样品和位点数量 方法:bcftools +counts xxx.vcf $ bcftools +counts Chr.recode.vcf Number of samples: 2232 Number of SNPs: 698763 Number of INDELs: 44021 Number ...
修改vcf.gz染色体编号方式 nohup bcftools annotate --rename-chrs chr_id.txt xx.vcf.gz -Oz -o xxx.vcf.gz --threads 23 & 统计vcf中样品和位点数量 方法:bcftools +counts xxx.vcf $ bcftools +counts Chr.recode.vcfNumber of samples: 2232Number of SNPs: 698763Number of INDELs: 44021Number of MN...
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/...
bcftools 是一个用于操作和处理 VCF/BCF 文件的软件工具集。它是 samtools 工具集的一部分,用于对比对后的 BAM 文件进行 SNP 和 Indel 的检测。bcftools 可...
Rename the short option-e, --error-probabilityfrom lower case to upper case-E, --error-probability Changes to the output format, replace the DC section with DCv2: adds a new column for the number of matching genotypes The--error-probabilityis newly interpreted as the probability of erroneous...
plugins Rename AFS to VRFS, variant read frequency score Mar 20, 2025 test Merge branch 'develop' of github.com:samtools/bcftools into develop Mar 20, 2025 .appveyor.yml Replace AppVeyor for GitHub Actions workflow for Windows builds Oct 21, 2024 .cirrus.yml Switch MacOS CI build to sonoma...
分支7 标签32 Petr DanecekMore informative error message, see #294132932f4年前 2338 次提交 .travis Update CI test configuration to recurse htslib submodules 4年前 doc Add new --mark-del, --mark-ins, and --mark-snv options. Resolves #1381 and #1170 ...
nohup bcftools annotate --rename-chrs chr_id.txt xx.vcf.gz -Oz -o xxx.vcf.gz --threads 23 & 统计vcf中样品和位点数量 方法:bcftools +counts xxx.vcf $ bcftools+counts Chr.recode.vcf Numberofsamples:2232NumberofSNPs:698763NumberofINDELs:44021NumberofMNPs:0Numberofothers:0Numberofsites:742784 ...
vcfindex.c 8.55 KB 一键复制 编辑 原始数据 按行查看 历史 Petr Danecek 提交于 5年前 . Rename the option --output-file to --output to make it consistent … 12345678910111213141516171819202122232425262728293031323334353637383940414243444546474849505152535455565758596061626364656667...