bcftools筛选条件分基础参数和高级表达式两种，这里用真实数据场景举例说明。基础参数直接加在命令行里，比如筛选染色体位置用-r参数，指定区域用-R参数，过滤样本用-S参数。筛选变异类型用–types参数，指定SNP或INDEL，处理多等位位点用–min-alleles和–max-alleles。筛选质量值时，QUAL字段和INFO里的MQ、QD要分开处理...
bcftools query -s ${samp} -f '[%TGT]' ${vcf} printf '\n' done > test.fa This works, except that any sites for which the reference is called has a '.', rather than the ref. allele. Is there a way to extract the ref allele genotype at these sites?
ID=@file .. selects lines with ID present in the file INFO/TAG=@file.txt .. selects lines where TAG has a string value listed in the file INFO/TAG!=@file.txt .. TAG must not have a string value listed in the file Allow to query REF,ALT columns directly, for example-e 'REF=...
使用bcftools query -l test.vcf > 453.list 将vcf文件中的样品名提取出来 不使用软件：head -100 all.vcf |grep "#C" |cut -f10-|xargs -n 1 > wild.txt 使用sh脚本 将453份数据写入变量$sample for sample in $(cat 453.list);创建每个样本的list文件 do to...
s); else if ( ret>0 ) error("The sample not found in the VCF: %s\n", ret==1 ? args->query_sample.name : args->control_sample.name); if ( args->control_sample.name ) free(tmp.s); } args->query_sample.idx = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_...
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/convert.c at 6b4
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/mpileup.c at 6b4
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/vcfsom.c at 6b4e
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/vcfstats.c at 6b
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix. - pysam/bcftools/vcfsort.c at 6b4