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...
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....
samtools: mpileup and other tools for handling SAM, BAM, CRAM bcftools: calling and other tools for handling VCF, BCF See alsohttp://github.com/samtools/ Building Samtools SeeINSTALLfor complete details.Release tarballscontain generated files that have not been committed to this repository, so bui...
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...
(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为bam或sam格式。 bam文件优点:bam文件为二进制文件,占用的磁盘空间比sam文本文件小;利用bam二进制文件...
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>] ...
view SAM<->BAM<->CRAM conversion depad convert padded BAM to unpadded BAM 2.1 构建索引(Indexing) dict-- 对fasta格式的参考基因组序列构建字典索引 $ samtools dict About: Create a sequence dictionary file from a fasta file Usage: samtools dict [options] <file.fa|file.fa.gz> ...
quickcheck quickly check if SAM/BAM/CRAM file appears intact fastq converts a BAM to a FASTQ fasta converts a BAM to a FASTA -- Statistics bedcov read depth per BED region depth compute the depth flagstat simple stats idxstats BAM index stats ...
HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and ...