–remove-indels即保留或去除SNP,留下INDEL。 根据VCF文件第七列FILTER进行过滤 –remove-filterer-allFILTER列除了PASS保留,其余都过滤 –keep-filtered,–remove-filtered保留或去除特定FILTER标签。可多次使用。 根据vcf第八列INFO进行过滤 –keep-INFO –remove-INFO根据INFO列的指定tag进行过滤 根据ALLEL进行过滤 –...
then the “–keep” option is executed before the “–remove” option. When multiple files are provided, the union of individuals from all keep files subtracted
VCFtools - v0.1.13 (C) Adam Auton and Anthony Marcketta 2009 Parameters as interpreted: --vcf all.gatk.fliter.vcf --out watermelon.pi --site-pi --remove-filtered-geno-all After filtering, kept 19 out of 19 Individuals Outputting Per-Site Nucleotide Diversity Statistics... After filtering,...
1. 下载安装VCFtools 在官网(https://vcftools.github.io/index.html)下载VCFtools安装包,下载地址链接为https://vcftools.github.io/downloads.html,该网页内界面如下所示,方框内为下载按钮。如果点击的是View On GitHub需要进入release中寻找最新版本(https://github.com/vcftools/vcftools/releases/tag/v0.1.16)。
--indv--remove-indv Specify an individual to be kept or removed from the analysis. This option can be used multiple times to specify multiple individuals. If both options are specified, then the "--indv" option is executed before the "--remove-indv option". ...
--indv <string> --remove-indv <string> Specify an individual to be kept or removed from the analysis. This option can be used multiple times to specify multiple individuals. If both options are specified, then the "--indv" option is executed before the "--remove-indv option". --...
(e.g. the total depth may need to be recalculated if individuals are removed). This behavior may be overriden by the following options. By default, BCF files are written out as BGZF compressed files. But that will remove the INFO fields as explained above, so just use normal te...
2 --max-alleles 2 \ --remove-indels 2>vcftools.log| gzip - >myresult/nohup1.vcf.gz & ...
如果不加–recode,会报错Keeping individuals in ‘keep’ list 提取某些样本的信息 vcftools --vcf rename_rs_samples_filtered.vcf --remove skip_samples.tsv --recode --out new.vcf skip_samples.tsv为一行一个样本 4.提取某个区间的信息 vcftools --gzvcf /bioinfo/data/1000G/rawData/20130502/20130502...
--remove-indv Specify an individual to be kept or removed from the analysis. This option can be used multiple times to specify multiple individuals. If both options are specified, then the "--indv" option is executed before the "--remove-indv option". ...