(1)官方使用说明文档 ./fcgene --gens example/example.chr22.impute2 --thresh0.9\--info example/example.chr22.impute2_info\--info-thresh info_thresh_value\--maf-thresh maf_thresh_value\--filter-snphwe=1e-2\--pedinfo example/impute.pedinfo\--oformatplink --outexample/impute_plink • ...
bcftools view -i "F_MISSING <= 0.2" 相当于vcftools的max-missing 0.8 或者用bcftools filter -e "F_MISSING > 0.2" 相当于vcftools的max-missing 0.8 bcftools view input/input.recode.vcf.gz -S 170.ID -i "F_MISSING <= 0.5" MAF bcftools filter -e "MAF < 0.05" input.vcf vcftools --vcf ...
、、、 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...
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 +fill-tags test.vcf -Ov -o annt_test.vcf -- -t AF,MAF,TYPE ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##contig=<ID=1,length=249250621> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ...
bcftools filter: Make --SnpGap optionally filter also SNPs close to other variant types. (#1126) bcftools gtcheck: Complete revamp of the command. The new version is faster and allows N:M sample comparisons, not just 1:N or NxN comparisons. Some functionality was lost (plotting and cluster...
bcftools view -i'%ID!="." & MAF\[0\]<0.01' 用bcftools进行突变筛选的示例 摘自公众号生信开发者 #选出位于bed文件中的所有区域的突变位点 bcftools view -R target.bed sample.filter.vcf.bgz #选出INFO中SAO=1的所有位点 bcftools view -i 'SAO=1' sample.filter..b37.vcf ...
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
[W::vcf_parse] FILTER 'SB1' is not defined in the header [W::vcf_parse] FILTER 'DETP20' is not defined in the header [W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String [W::vcf_parse] INFO 'SOMATIC' is not defined in the header, assuming Type=...