bcftools的subset和F_MISSING过滤,一定要分两步做,不然会出错: bcftools view -S kee.ID input.vcf | bcftools filter -e "F_MISSING > 0.2" > output.vcf #分两步过滤 #相当于 vcftools --vcf input.vcf --max-missing 0.8 --keep keep.ID --recode --out output ...
特定区域的过滤:如果您只想对特定染色体区域的变异进行过滤,可以使用-r选项指定区域。 代码语言:javascript 复制 bcftools filter-r chr1:1000-2000-e'QUAL > 20'input.vcf.gz-o filtered_region.vcf 其他选项:bcftools还提供其他选项,例如基于频率的过滤和过滤特定基因型的变异。您可以查阅bcftools的官方文档以获取...
我在linux终端中的原始输入是 bcftools filter -e 'TYPE="snp"' input1.vcf -O v -o output1.filter.vcf bcftools filter -e 'TYPE="snp"' input2.vcf -O v -o output2.filter.vcf bcftools filter -e 'TYPE="snp"' input3.vcf -O v -o output3.filter.vcf bcftools filter - 浏览0提问于201...
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-R, --ignore-RG ignore RG tags (one BAM = one sample) #忽略BAM文件中的@RG信息,认为一个BAM文件就是一个样品的数据 --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset [] --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set ...
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 ...
set->filter = filter_init(set->hdr, args->filter_str); } args->hdr_out = tmp_hdr; free(str.s); } static void destroy_data(args_t *args) { bcf_hdr_destroy(args->hdr_out); free(args->info_tags); free(args->fmt_tags); ...
new ILEN filtering expression to be able to filter by indel length new MEAN, MEDIAN, MODE, STDEV, phred filtering functions new formatting expression %PBINOM (phred-scaled binomial probability), %INFO (the whole INFO column), %FORMAT (the ...
case 's': args->strict_filter = 1; break; case 'f': args->ref_fname = optarg; break; case 'r': args->region = optarg; break; case 'R': args->region = optarg; region_is_file = 1; break; case 't': args->targets = optarg; break; case 'T': args->targets = opt...
bcftools view -i 'SAO=1' sample.filter..b37.vcf #选出INFO中AC>2的所有位点 bcftools view -i "AC>=2" ExAC.r1.sites.vep.vcf.gz #选出遗传方式是AR或XR的位点(需INFO字段中已有INHERITANCE注释) bcftools view -i 'INHERITANCE\[*\] = "AR" || INHERITANCE\[*\] = "XR"' sample.filter....