基因数据处理35之使用samtools和bcftools进行变异分析2--连续处

指令：

samtools mpileup -uf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058_longer.sorted.bam | bcftools call -mv > NA12878_snp_A2G_chr20_225058_longer.raw.vcf

bcftools filter -s LowQual -e '%QUAL<20 || DP>100' NA12878_snp_A2G_chr20_225058_longer.raw.vcf  > NA12878_snp_A2G_chr20_225058_longer.flt.vcf

结果：

xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ samtools mpileup -uf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058_longer.sorted.bam | bcftools call -mv > NA12878_snp_A2G_chr20_225058_longer.raw.vcf Note: Neither --ploidy nor --ploidy-file given,assuming all sites are diploid [mpileup] 1 samples in 1 input files <mpileup> Set max per-file depth to 8000 xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ bcftools filter -s LowQual -e '%QUAL<20 || DP>100' NA12878_snp_A2G_chr20_225058_longer.raw.vcf > NA12878_snp_A2G_chr20_225058_longer.flt.vcf xubo@xubo:~/xubo/data/avocado/NA12878_snp_A2G_chr20$ cat NA12878_snp_A2G_chr20_225058_longer.flt.vcf ##fileformat=VCFv4.2 ##FILTER=<ID=PASS,Description="All filters passed"> ##samtoolsVersion=1.3.1-24-gf458b7c+htslib-1.3.1-35-g481752c ##samtoolsCommand=samtools mpileup -uf Homo_sapiens_assembly19chr20.fasta NA12878_snp_A2G_chr20_225058_longer.sorted.bam ##reference=file://Homo_sapiens_assembly19chr20.fasta ##contig=<ID=20,length=63025520> ##ALT=<ID=*,Description="Represents allele(s) other than observed."> ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> ##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel"> ##INFO=<ID=IMF,Type=Float,Description="Maximum fraction of reads supporting an indel"> ##INFO=<ID=DP,Description="Raw read depth"> ##INFO=<ID=VDB,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> ##INFO=<ID=RPB,Description="Mann-Whitney U test of Read Position Bias (bigger is better)"> ##INFO=<ID=MQB,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)"> ##INFO=<ID=BQB,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)"> ##INFO=<ID=MQSB,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)"> ##INFO=<ID=SGB,Description="Segregation based metric."> ##INFO=<ID=MQ0F,Description="Fraction of MQ0 reads (smaller is better)"> ##FORMAT=<ID=PL,Number=G,Description="List of Phred-scaled genotype likelihoods"> ##FORMAT=<ID=GT,Type=String,Description="Genotype"> ##INFO=<ID=ICB,Description="Inbreeding Coefficient Binomial test (bigger is better)"> ##INFO=<ID=HOB,Description="Bias in the number of HOMs number (smaller is better)"> ##INFO=<ID=AC,Number=A,Description="Allele count in genotypes for each ALT allele,in the same order as listed"> ##INFO=<ID=AN,Description="Total number of alleles in called genotypes"> ##INFO=<ID=DP4,Number=4,Description="Number of high-quality ref-forward,ref-reverse,alt-forward and alt-reverse bases"> ##INFO=<ID=MQ,Description="Average mapping quality"> ##bcftools_callVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c ##bcftools_callCommand=call -mv ##FILTER=<ID=LowQual,Description="Set if true: %QUAL<20 || DP>100"> ##bcftools_filterVersion=1.3.1-15-g7c7c7a2+htslib-1.3.1-35-g481752c ##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=1;HOB=0.5;AC=1;AN=2;DP4=20,22,21;MQ=60 GT:PL 0/1:255,255
20  224971  .   G   A   222 PASS    DP=85;VDB=0.260887;SGB=-0.693145;RPB=0.8548;MQB=0.982719;MQSB=0.980987;BQB=0.276682;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=23,19,20,21;MQ=59    GT:PL   0/1:255,255
20  225058  .   A   G   217 PASS    DP=81;VDB=0.824099;SGB=-0.693139;RPB=0.952244;MQB=0.978845;MQSB=0.987634;BQB=3.33479e-07;MQ0F=0;ICB=1;HOB=0.5;AC=1;AN=2;DP4=25,14,21,15;MQ=59   GT:PL   0/1:250,255

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