when I use the command 'samtools view -bS GSM653001_BMM_KO_aligned.SAM > GSM653001_BMM_KO_aligned.bam' I got an error as follows: [E::sam_parse1] missing SAM header [W::sam_read1] Parse error at line 3 [main_samview] truncated file. the header of SAM file using command 'samto...
In this case samtools view and samtools index failed in open the file "20201032_sorted.sam" , because this file should be the output of samtools sort. Which in turn, cannot can not read the header of the input file "20201032.sam" . The header of the sam file looks as follows: @sqS...
head test.sam The first 10 lines on your terminal after typing "head test.sam", should be lines starting with an "@" sign, which is an indicator for a header line. If you don't see lines starting with the "@" sign, the header information is most likely missing. If the header info...
BAM是一种压缩的二进制格式,占用更少的存储空间;同时由于其压缩性质,BAM文件在数据检索时通常比SAM文件更高效。 ##简单对比感受一下sam和bam占用存储空间大小的差别 ## 原始文件大小 2.5G 12月 12 11:04 d0_1.fastq.gz 2.7G 12月 12 11:05 d0_2.fastq.gz ## 产生的sam文件大小 27G 12月 12 12:00...
dict_with_accession.dict human_g1k_v37_chr1_59kb.fasta ordered.sam small.bam unmapped.sam example_intervals.list improper_pairs_1.fq parquet_lister_dir_empty small_missing.vcf unordered.sam fastq_noqual.fq improper_pairs_2.fq proper_pairs_1.fq small_realignment_targets.intervals unsorted.sam ...
This command will exit with a non-zero exit code if any input files don't have a valid header or are missing an EOF block. Otherwise it will exit successfully (with a zero exit code). Options: -v Verbose output: will additionally print the names of all input files that don't pass ...
-H, --no-header do not print @HD line -o, --output FILE file to write out dict file [stdout] -s, --species STR species -u, --uri STR URI [file:///abs/path/to/file.fa] 对基因组文件建立一个序列字典文件 $samtools dict -o hg19.dict hg19.fa ...
view命令中,对sam文件头部的输入(-t或-T)和输出(-h)是单独的一些参数来控制的。 Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]默认情况下不加 region,则是输出所有的 region. Options: -b output BAM 默认下输出是 SAM 格式文件,该参数设置输出 BAM 格式 -h print header for...
本文整理了Java中htsjdk.samtools.SAMRecord.getHeader()方法的一些代码示例,展示了SAMRecord.getHeader()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台,是从一些精选项目中提取出来的代码,具有较强的参考意义,能在一定程度帮忙到你。SAMRecord.getHeader()方法的具体详情如下:包路径:htsjdk....
类名称:SAMFileHeader 方法名:setTextHeader SAMFileHeader.setTextHeader介绍 暂无 代码示例 代码示例来源:origin: com.github.samtools/htsjdk mFileHeader.setTextHeader(textHeader.toString()); 代码示例来源:origin: org.seqdoop/htsjdk mFileHeader.setTextHeader(textHeader.toString()); ...