samtools view -bS artificial.cram >artificial2.bam 1. 2. 3. 遇到问题: hadoop@Mcnode6:~/cloud/adam/xubo/1000genomes/GIH/NA21144/alignment$ samtools view -b -S NA21144.alt_bwamem_GRCh38DH.20150718.GIH.low_coverage.cram >NA21144.alt_bwamem_GRCh38DH.20150718.GIH.low_coverage.bam [E::...
view SAM<->BAM<->CRAMconversion depad convert paddedBAMto unpaddedBAMsamples list the samplesinasetof SAM/BAM/CRAMfiles--Mischelp[cmd]displaythishelp message or helpfor[cmd]version detailed version information 这里看到基础命令主要分为六个模块,分别为索引、编辑、文件操作、统计、视图以及其他。这里想...
Hello, I'm having a problem using samtools view to convert from cram to bam. A small fraction of the records in the resulting bam files appear to have the "bin" field set to an incorrect value. (This shows up as error messages from Picar...
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 2.3.2)samtools fastq RNA-seq.bam >RNA-seq.fq #将bam 文件转化为fastq 2.3....
本命令对bam文件建立索引并产生后缀为.bai的文件，用于快速的随机处理。很多后续分析的过程需要有bai文件的存在，特别是显示序列比对情况下，比如samtool的tview命令等。（5） view：SAM<->BAM<->CRAM conversion （6）depth：compute the depth 本命令对bam文件中的每个碱基位点的测序深度进行统计，并...
#必须对bam文件进行默认情况下的排序后,才能进行index。否则会报错。 $ samtools index aln.sorted.bam (5) view:SAM<->BAM<->CRAM conversion 本命令将sam文件转换成bam文件;然后对bam文件进行各种操作,比如数据的排序和提取(这些操作是对bam文件进行的,不能对sam文件进行该操作);最后将排序或提取得到的数据输出...
view SAM<->BAM<->CRAMconversion depad convert paddedBAMto unpadded BAM 一、samtools view功能 1、将sam文件转化为bam文件 samtools view -bS in.sam > in.bam 是view的一个应用-b指定输出文件为bam, -S 指定输入文件为sam 2、查看bam文件的header信息 ...
samtools: mpileup and other tools for handling SAM, BAM, CRAM bcftools: calling and other tools for handling VCF, BCF See also http://github.com/samtools/ Building Samtools See INSTALL for complete details. Release tarballs contain generated files that have not been committed to this repository,...
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] <in.bam> [<prefix>] ...
sambamba 不仅可以对 BAM 文件进行排序、索引、过滤、统计、标记重复等常见的操作,还可以进行一些特殊的功能,比如区域过滤,标记重复序列,检测结构变异等。sambamba 还支持多种输入和输出格式,比如 CRAM、SAM、BED、VCF 等,让我们可以灵活地处理各种数据类型。 此外,sambamba...