What is in samtools?

What is in samtools?

Samtools is a set of utilities that manipulate alignments in the SAM (Sequence Alignment/Map), BAM, and CRAM formats. It converts between the formats, does sorting, merging and indexing, and can retrieve reads in any regions swiftly. Samtools is designed to work on a stream.

How does a SAM file look like?

The SAM format consists of a header and an alignment section. The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. SAM files can be analysed and edited with the software SAMtools.

What does samtools index do?

samtools “index” Indexing a genome sorted BAM file allows one to quickly extract alignments overlapping particular genomic regions. Moreover, indexing is required by genome viewers such as IGV so that the viewers can quickly display alignments in each genomic region to which you navigate.

What is NM tag BAM file?

A BAM file (*. bam) is the compressed binary version of a SAM file that is used to represent aligned sequences up to 128 Mb.

What does samtools Fixmate do?

samtools fixmate – fills in mate coordinates and insert size fields.

What information is in a BAM file?

sequence alignment data
A BAM file (. bam) is the binary version of a SAM file. A SAM file (. sam) is a tab-delimited text file that contains sequence alignment data.

What is in a SAM file?

SAM files are a type of text file format that contains the alignment information of various sequences that are mapped against reference sequences. These files can also contain unmapped sequences. Since SAM files are a text file format, they are more readable by humans and will be used as the examples for this section.

What is samtools bioinformatics?

SAMtools is a library and software package for parsing and manipulating alignments in the SAM/BAM format. It is able to convert from other alignment formats, sort and merge alignments, remove PCR duplicates, generate per-position information in the pileup format (Fig.

How long does samtools sort take?

We compared the sorting speed of a 25Gb unsorted BAM file with SAMtools and sambamba. Our results show that sambamba was 2x faster than SAMtools. The following violin plot shows that SAMtools took 20 minutes while sambamba could sort the same file in 10 minutes.

What does samtools collate do?

A faster alternative to a full query name sort, collate ensures that reads of the same name are grouped together in contiguous groups, but doesn’t make any guarantees about the order of read names between groups.

What does SAMtools Fixmate do?

What is a SAM header?

SAM stands for Sequence Alignment/Map format. It is a TAB-delimited text format consisting of a header section, which is optional, and an alignment section. If present, the header must be prior to the alignments. Header lines start with ‘@’, while alignment lines do not.

What is a page header in APA style?

For professional papers, the page header consists of the page number and running head. Follow these guidelines to include page numbers in both student and professional APA Style papers:

What are headings in APA format?

Headings are used to help guide the reader through a document. The levels are organized by levels of subordination, and each section of the paper should start with the highest level of heading. There are 5 heading levels in APA. The 6th edition of the APA manual revises and simplifies previous heading guidelines.

What alignments are supported in SAMtools (1)?

Only include alignments that match the filter expression STR . The syntax for these expressions is described in the main samtools (1) man page under the FILTER EXPRESSIONS heading. Only output alignments with all bits set in FLAG present in the FLAG field.

How do I output header in SAM format?

Include the header in the output. Output the header only. When producing SAM format, output alignment records but not headers. This is the default; the option can be used to reset the effect of -h / -H . Instead of printing the alignments, only count them and print the total number.