Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts withftp://' orhttp://'. Samtools checks the current working directory for the index file and will download the index upon absence. Samtools does not retrieve the entire alig...
Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of
Samtools is also able to open a BAM (not SAM) file on a remote FTP or HTTP server if the BAM file name starts with `ftp://' or `http://'. Samtools checks the current working directory for the index file and will download the index upon absence. Samtools does not retrieve the entir...
以上可以得到每条染色体所有位点覆盖度和测序深度的总和,将它们处于染色体的长度就得到了每条染色体平均的测序深度和各个染色体的覆盖度,其中chromosome的长度在bam文件里面可以看到,用samtools view -H input.bam 即可。7.2. 以WIG文件输出测序深度 目录samtools depth SRR1042593.sorted.bam | perl -ne 'BEGIN{ print ...
Return non-zero error code when the input BAM/CRAM file is truncated (#2177) AddFORMAT/ADannotation by default, disable with-a -AD bcftools norm Support realignment of symbolic<DUP.*>alleles, similarly to<DEL.*>added previously (#1919,#2145) ...
samtools tview aln.sorted.bam ref.fasta samtools split merged.bam samtools quickcheck in1.bam in2.cram samtools dict -a GRCh38 -s "Homo sapiens" ref.fasta samtools fixmate in.namesorted.sam out.bam samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam ...
change size_t to uint32_t in bam_header_t This may cause issues on 64-bit big-endian machines. Reported and fixed by Paolo Emilio Mazzon. commit af31bf5a78aea03baf6eb90fe50076549d499f6e Author: Heng Li <lh3@live.co.uk> Date: Mon Sep 26 20:17:57 2011 -0400 rename pad...
本文整理了Java中htsjdk.samtools.SAMRecord.setMappingQuality()方法的一些代码示例,展示了SAMRecord.setMappingQuality()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.setMappingQuality()方法的具体详情如下...
2.5 samtools split:通过read group 对一个文件进行分割 2.6 samtools mpileup:从一个比对结果中产生plieup的文本格式的文件 2.7 samtools coverage:产生每个染色体上的覆盖度的柱形图和表格 2.8 samtools markdup:在sort好的bam中标记出重复的比对 附:SAM格式的详细说明 ...
samtools split merged.bam samtools quickcheck in1.bam in2.cram samtools dict -a GRCh38 -s "Homo sapiens" ref.fasta samtools fixmate in.namesorted.sam out.bam samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam ...