#!/bin/bash # 输入BAM文件 input_bam="your_input.bam" # 输出目录 output_dir="split_bams" mkdir -p $output_dir # 获取BAM文件中的染色体列表 chromosomes=$(samtools view -H $input_bam | grep '^@SQ' | cut -f 2 | cut -d: -f 2) # 遍历每个染色体并拆分BAM文件 for chr in $chromos...
command = f"samtools mpileup -f {reference_file} {bam_file}" return subprocess.Popen(shlex.split(command), stdout=subprocess.PIPE, stderr=subprocess.PIPE) # 调用 samtools mpileup 并打印输出信息 def process_mpileup_output(bam_file, reference_file): process = run_mpileup(bam_file, reference_fil...
生物信息学必备技能:一文解锁Samtools 高通量测序技术让生物信息学领域数据量激增,如何高效处理这些数据成了科研人员和学生的难题。在众多工具中,Samtools 表现亮眼,不管是基因组学还是转录组学研究,都能助力数据处理。它到底有什么厉害之处?接下来,一起深入了解这个强大工具集。 SAMtools 是一个由李恒博士开发的开源软...
sort sort alignment file split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA collate $samtools collate Usage: samtools collate [-Ou] [-o <name>] [-n nFiles] [-l cLevel] <...
samtools split test.sort.bam 13、quickcheck 作用:检查SAM/BAM/CRAM文件的完整性 用法: samtools quickcheck -v *.bam > bad_bams 14、fastq 作用:bam文件转换为fastq 用法: samtools fastq test.bam 15、fasta 作用:bam文件转换为fasta 用法: samtools fasta test.bam ...
split splits a file by read group quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA 示例 2.3.1)samtools sort -nRNA-seq.bam>RNA-seq_sorted_out.bam #将bam文件进行排序 ...
(for fosmid pool only) addreplacerg adds or replaces RG tags markdup mark duplicates -- File operations collate shuffle and group alignments by name cat concatenate BAMs merge merge sorted alignments mpileup multi-way pileup sort sort alignment file split splits a file by read group quickcheck ...
split splits a filebyreadgroupquickcheck quicklycheckif SAM/BAM/CRAM file appears intact fastq converts a BAMtoa FASTQ fasta converts a BAMtoa FASTA-- Statisticsbedcov read depthperBED region depth compute the depth flagstat simple stats
bwa主要用于将低差异度的短序列与参考基因组进行比对。主要包含三种比对算法:backtrack、SW和MEM,第一种只支持短序列比对(<100bp),后两种支持长序列比对(70bp~1M),并支持分割比对(split alignment)。MEM算法是最新的也是官方推荐的。 BWA-MEM 是一种新的比对算法,用于将测序 reads 或者组装后 contigs 比对至大型...
call_splitSee protocol […] and InDels was done using GATK Unified Genotyper, which uses a Bayesian genotype likelihood model to report alleles and Phred-scaled confidence values []. Variants (SNVs and indels) were called withSAMTools, with reference to public databases including dbSNP and 1000Ge...