-C:求第一个文件有其他文件没有的集合 -f:可筛选FILTER列的信息,如果想筛选PASS的记录可以用 -f PASS 1. 查看VCF文件中的样本的名称 bcftools query -l merge.indel.filter.vcf.gz 2. 将含有多个样本的vcf文件拆分成单个样本的vcf文件 # 准备样本list文件sampleListName.txt sample1 sample2 sample3 # 拆分...
-s / --soft-filter:将过滤掉的位点用字符串注释 bcftoolsfilter--no-version-sFLTER-i'(%QUAL>20 && format/DP>4 && MQ>30)||(GT="0/0")'-Ov-oBL48384.Raw.flt.vcfBL48384.Raw.vcf.gz bcftoolsfilter-i'FILTER=="PASS"'--no-version-Ov-oBL48384.Raw.flter.vcfBL48384.Raw.flt.vcf --no...
1. 显示VCF文件的头信息 bcftools view -h sample.vcf##fileformat=VCFv4.2##FILTER=<ID=PASS,Description="All filters passed">##bcftoolsVersion=1.5+htslib-1.5##bcftoolsCommand=mpileup -f /public/analysis/ucsc.hg19.fasta -Ou /public/analysis/result/sample.bam##reference=file:///public/analysis/uc...
$ bcftools filter -i ' FILTER=="PASS" && DP>20 && GQ>100 && QUAL>100' "$outDIR"_norm/"$out_basen (3) 提取 突变位点的AD和DP,顺便可以计算 VAF: $ bcftools query-f'[%AD]\n'"$outDIR"/"$out_basename"|awk'BEGIN{FS=","}{ print $2 }'>>"$outDIR"_tmp/"$out_basename"_AD...
##bcftools_filterCommand=filter -s LowQual -e '%QUAL<20 || DP>100' NA12878_snp_A2G_chr20_225058_longer.raw.vcf #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 20 224941 . T A 222 PASS DP=86;VDB=0.47247;SGB=-0.693146;RPB=0.883981;MQB=1;MQSB=1;BQB=0.913137;MQ0F=0;ICB...
FILTER!~"A" Neither "A" nor "A;B" pass Fix in commutative comparison operators, in some cases reversing sides would produce incorrect results (#1224; #1266) Better support for filtering on sample subsests Add SMPL_*/S* family of functions that evaluate within rather than across all sampl...
FILTER INFO FORMAT A# concat-a.vcf文件位点1100.GTTT G1806q10 DP=35GT:GQ:DP0/1:409:351110.C T,G1792PASS DP=32GT:GQ:DP0/1:245:321120.GA G628q10 DP=21GT:GQ:DP1/1:21:211130.GAA GG1016PASS DP=22GT:GQ:DP0/1:212:221140.GT G727PASS DP=30GT:GQ:DP0/1:150:301150.TAAAA ...
Consider the following simple VCF file: ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##contig=<ID=1,length=249250621> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> #CHROM POS ID REF ALT QUAL FIL...
bcftools.20170319.NA12878.vcf.gz / *selecting...-e'INFO/DP<5' input.vcf / #printing out variants that pass the filter: ~/bin/bcftools/bcftools view...,PASS lc_bams.bcftools.20170411.exc.norm.SNP.filtered.vcf.gz / #bcftools stats and filtering: ~/bin/bcftools 1.1K20 bcftools学习笔记...
2. 根据条件进行筛选,比如:筛选出FILTER列是PASS的,DP >20 , GQ >100, QUAL >100的位点: bcftools filter-i' FILTER=='PASS' && DP>20 && GQ>100 && QUAL>100''$outDIR'_norm/'$out_basename'--output'$outDIR'/'$out_basename'--output-type z ...