3. bcftools call[OPTIONS]FILE 变异检测,输入文件为VCF/BCF文件,常与bcftools mpileup连用。 bcftools mpileup -Ou -f REF.fa reads.bam | bcftools call -mv -Oz -o reads.vcf.gz -g, --gvcfINT:输出GVCF文件 -G FILE:以群体进行变异检测 4. bcftools cnv 检测拷贝数变异,输入文件为vcf文件需要BAF(B-...
bcftools 作为实用的变异查找工具, 可以查找指定区域的变异; 相比于GATK可以互相补充。 1. conda 安装 conda install bcftools -y 2. bcftools 查找变异位点bcftools mpileup -r chr22:38519150-385191650 \ -f /public/analysis/reference/hg19/hg19.fa \...
基因组文件格式为.bam,callsnp之后,再转换为.fq.gz格式才能做为PSMC输入文件 bcftools mpileup 和 bcftools call可以进行SNP calling, bcftools mpileup -Ou -I -f ref.fa .sorted.mardup.bam | bcftools call -c -Ov | vcfutiles vcf2fq -d 10 -D 100 | gzip > dilpoid.fq.gz 需要注意的是mpileup...
bcftools mpileup -a AD,QS -f ref.fa -Ou proband.bam father.bam mother.bam | \ bcftools call -mv -Ou | \ bcftools +trio-dnm -p proband,father,mother -Oz -o output.vcf.gz This new version also implements the DeNovoGear model. The original behavior of trio-dnm is no longer suppor...
mpileup: include reads with unlisted or missing RG ID to match previo… Aug 5, 2016 bcftools.h Keep only one implementation of calc_binom() Aug 6, 2024 bin.c Check the return status of hts_readlist and warn about non-existent f… Jan 7, 2022 bin.h stats: make the AF binning code...
bcftools call SNP /share/work/biosoft/bcftools/latest/bin/bcftools mpileup -a 'AD,DP' -Ou -f /share/work/database/ref/Triticum_aestivum/IWGSC_v2.1/iwgsc_refseqv2.1_gene_annotation_200916/iwgsc_refseqv2.1_assembly.fa /share/nas1/renzx/project/zx-20210524-20_BSR_2xiaomai/ref/ann/9.SNP_...
三、SNP calling $ samtools mpileup -uf Trinity-longest.fasta aln-6.sorted.bam | bcftools call -Ou -mv > var.raw.bcf $ bcftools view var.raw.bcf | bcftools filter -e 'QUAL<30 || DP<20' > val.filter.vcf $ bcftools view val.filter.vcf | bcftools filter -i 'TYPE="snp"' > val...
bcftools mpileup-Ou-I-fref.fa.sorted.mardup.bam|bcftools call-c-Ov|vcfutiles vcf2fq-d10-D100|gzip>dilpoid.fq.gz 需要注意的是mpileup命令虽然也会输出vcf格式文件,但是并不直接进行snp calling。 下面的命令可以生成vcf格式文件 bcftools mpileup -I -f ref.fa .sorted.markdup.bam > mpileup.vcf ...
bcftools mpileup-Ou R1.sorted.bam-f ref.fa|bcftools call-mv-o raw.vcf## 参数-f:指定参考基因组-b:bam list的文件,样本较多时可以使用-C:--adjust-MQ 矫正的MQ值,推介50-q:--mim-MQ MQ质量值-Q:--min-BQ base质量值-r:--regions call 特定染色体或者区域的变异;如chr1;chr1:100-20000-R:...
3-生成baw文件 bwa mem -t 10 nip_all.chrs.con.fasta sra1_1.fastq sra1_2.fastq | samtools view -bS -@ 10 -o sra1.bam 4-排序 for file in *.bam;do samtools sort $file -@ 5 -o $file"sorted.bam";done 5-callsnp bcftools mpileup -Ou -f nip_all.chrs.con.fasta sra1.sorted....