#out.vcf.gz文件头的contig字段和变异位点的染色体号都会被转换 bcftools annotate --rename-chrs {GRCh37_to_hg19.txt} -Oz -o {out.vcf.gz} {input.vcf.gz} chr_name_change.txt文件格式示例(GRCh37转hg19): 四、bcftools提取vcf中指定字段 应用场景:数据库简化, 比如GnomAD, clinvar 运行方式: #排除法...
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...
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...
New-s, --samplesoption to include the#CHROMheader line with samples. bcftools gtcheck Add output options-o, --outputand-O, --output-type Add filtering options-i, --includeand-e, --exclude Rename the short option-e, --error-probabilityfrom lower case to upper case-E, --error-probabilit...
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...
Rename the option--output-fileto--outputto make it consistent … 5年前 vcfisec.c Autodetected output file type from the output file suffix (e.g. .bcf, … 4年前 vcfmerge.c Makemerge -Rbehavior consistent with other commands and
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 ...
--rename-chrsfile:旧名字 新名字 空格分隔,一行一个染色体。染色体换名 3. bcftools call[OPTIONS]FILE 变异检测,输入文件为VCF/BCF文件,常与bcftools mpileup连用。 bcftools mpileup -Ou -f REF.fa reads.bam | bcftools call -mv -Oz -o reads.vcf.gz ...
case 11 : args->rename_annots = optarg; break; case 12 : args->min_overlap_str = optarg; break; case 13 : case 'W': if (!(args->write_index = write_index_parse(optarg))) error("Unsupported index format '%s'\n", optarg); break;8...