$ samtools view -Sb A.sam > A.bam #转为bam文件 $ samtools sort A.bam > A_sort.bam #排序 $ samtools view -h A_sort.bam > A_sort.sam #再转回来sam文件,一定要加-h参数,默认是不输出header的。如果没有-h参数,是无法对sam文件进行转换和排序的。如下: [E::sam_parse1] missing SAM header
Nov 03, 2014 · After converting the .bam file into the .sam format, our script extracts a predefined amount of reads, writes them back into a sorted .bam file and finally creates a .bai index file from it. The extraction filters for reads on a given chromosome, with a start position in between a given range.

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The header in TopHat BAM files now correctly lists the sort order as coordinate, with group order reference; Update - TopHat 1.1.0 packages. The build of 1.1.0 released yesterday was throwing an exception with single end reads. This has been corrected and the packages have been updated. New developers - Daehwan Kim and Geo Pertea
Saving to BAM files from a BioMap object ?. Learn more about bioinformatics, bam format Bioinformatics Toolbox

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Associate BAM files with samples in the VCF file using a 2 column tab-delimited mapping file. The filename must be <vcf file name>.mapping. In other words add .mapping to the end of the vcf file name. The first column is the sample name from the vcf file, the second the path to the bam file. The bam file path can be a URL or file path, and it ...
bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. If you have any questions please use the bamUtil Google Group to ask questions or recommend improvements to bamUtil.

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BAM file to be sorted Step 2: BAM-to-SAM. BAM File to Convert. Output dataset 'output' from step 1 Include header in output ... No value found for 'Number of header ...
Hello Carlos, Start by converting your BAM file to SAM, with "NGS: SAM Tools -> BAM-to-SAM". It is probably best to include the header if you plan to use the SAM file in downstream tools later on. If not, you can skip the step where it is saved.

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BAM files store their header as plain-text SAM headers. However, they additionally store the name and length information about the reference sequences. This information is mandatory since in BAM, the alignment records only contain the numeric ids of the reference sequences. Thus, the name is stored outside the record in the header.
FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores.Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

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Reorder the header of the BAM file to match the reference. Sort the reads in the BAM file by coordinate. Mark duplicates in the BAM file and report duplicate metrics. Run up to 8 additional Picard tools. After running the tools, use picardmetrics collate to merge all of the generated metrics from multiple BAM files into tab-delimited files ...
Older versions of SAMtools posed challenges with PacBio BAM files. In particular, when merging BAM files, SAMtools output formerly did not include all of the read groups found in the input files, and it omitted the @HD::pb tag we use to indicate our version of the BAM spec from output (even when present in input).

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The BAM format is described in the SAM specification. SetChunk sets a limited range of the underlying BGZF file to read, after seeking to the start of the given chunk.
failed to open BamFile: SAM/BAM header missing or empty file: '03-192B3_lung.sort.nodup.bam.realigned.bam' In addition: Warning message: In doTryCatch(return(expr), name, parentenv, handler) : [bam_header_read] invalid BAM binary header (this is not a BAM file). I looked at the header data this way:

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A zip file consists of a central directory, which is like a table of contents that points backwards to individual files. Each file consists of a local file header and compressed file data. The headers in the central directory and in the files contain (redundant) metadata such as the filename. The zip file format specification is called APPNOTE ...
Message-ID: [email protected]od-1.library.ucsb.edu> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type ...

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Jul 15, 2015 · First, we need to provide a header file, which we can get from the original bam file. Then, we concatenate the header and the extracted uniquely mapped reads, based on the lack of XS tag. samtools view -H input.bam > header.sam samtools view -F 4 input.bam | grep -v "XS:" | cat header.sam - | \ samtools view -b - > unique.bam rm header.sam
The following examples show how to use htsjdk.samtools.SAMFileHeader.These examples are extracted from open source projects. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example.

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When the file is done being saved the final file information will be written to 18/6 offset $40 instead of 19/6 causing some directory corruption to the entry at 18/6. Also, the BAM entries for the sectors occupied by the new file will not be saved and the new file will be left as a SPLAT (*) file.
P.s. the bam file was sorted and indexed (both in .bai and .csi format) using samtools: samtools sort SNP.alignment.bam SNP.alignment.sorted samtools index SNP.alignment.sorted (or samtools index -c for .csi)
header (Optional) bamHeader. It's possible to provide a bamHeader for the new BAM file (in order to control the header entries in the new file). When no header is given, the header from the bamReader will be used. The 'SO' entry in the 'headerLine' (which gives information about the sorting status) segment will be altered.
If the header is absent from the SAM file use the command below, where reference.fa is the reference fasta file used to map the reads: ... #random BAM file mapped ...
BAM file handler, opened by bam_open(). Return Value. pointer to the header structure. bam_header_t::hash will be initialized if empty. bam_aux_get. Retrieve data of a tag.

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