基因型过滤标准:保留双等位基因(biallelic sites)以及次等位基因频率大于0.05的位点: bcftools view --types snps -m 2 -M 2 -q 0.05:minor genotypes.chr22.vcf | bgzip -c > genotypes.chr22.vcf.gz --types snps -m 2 -M 2 指的是保留双等位基因(biallelic sites); 0.05:minor 指的是次等位基因...
I'm looking for triallelic records, for which the allele count of one of the alleles is zero. I'm doing bcftools view --min-alleles 3 --max-ac 0:minor $vcf, but that prints all records. For example this one: 20 61279 rs189899941 C A,T . PASS AR2=0.884;DR2=0.907;AF=0.009,...
使用bcftools提取 do bcftools view -S list/$sample.list /public/home/lianglunping/work/SV/453.vcf>/public/home/lianglunping/work/SV/453/$sample.vcf;done
得到bcf文件以后，第二步执行命令：bcftools view -cNegv samtools_result.bcf > samtools_result.vcf 命令解释：veiw 是bcftools中主要的方法，‘Convert between BCF and VCF ， call variant candidates and estimate allele frequencies.’-c Call variants using Bayesian inference .-N Skip sites w...
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int main_vcfview(int argc, char *argv[]) { int c; args_t *args = (args_t*) calloc(1,sizeof(args_t)); args->argc = argc; args->argv = argv; args->files = bcf_sr_init(); args->clevel = -1; args->print_header = 1; ...
et341@login-sand1:/fortravis$ bcftools view -H temp3.vcf.gz | cut -f 1,2,4,5 10 101594176 C A Author eturro commented Dec 2, 2014 Perhaps we need to unnormalise with -m +any each individual file before merging in order to avoid duplicate records? I can try this: for each co...