What does samtools view do?
What does samtools view do?
The samtools view command is the most versatile tool in the samtools package. It’s main function, not surprisingly, is to allow you to convert the binary (i.e., easy for the computer to read and process) alignments in the BAM file view to text-based SAM alignments that are easy for humans to read and process.
What does samtools Fixmate do?
samtools fixmate – fills in mate coordinates and insert size fields.
How do I view a .BAM file?
For viewing BAM files, an index file must be found in the same directory as the BAM file. The index should be named by appending “. bai” to the BAM file name. If there is no index file, you can use SAMTools to create one (please download SAMTools from http://samtools.sourceforge.net and install locally).
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.
How do you use Samtools flags?
samtools can select reads according to their flags. When you want to select reads with a specific flag, none of this option only will get what you want. You can get what you want by combining -f and -F. For example, if you want a flag 67, which is 00001000011, the complement flag is 11110111100, which is 1980.
What language is Samtools written?
C
SAMtools/Programming languages
SAMtools [3, 4] is written in the C programming language and uses SAM/BAM files. It has various functions for manipulating SAM/BAM files, such as viewing, sorting, indexing, and pileup.
What is Fixmate?
FIXimate is an interactive Web browser based reference for the FIX Specification. web server or it can be downloaded and used locally.
Is BAM file sorted?
Most functionality while using BAM files can be described as such: BAM files are sorted by reference coordinates (samtools sort) Sorted BAM files are indexed (samtools index) Sorted, indexed BAM files are filtered based on location, flags, mapping quality (samtools view with filtering options)
Does samtools merge sort?
samtools merge – merges multiple sorted input files into a single output.
What is the SAMtools view command?
The samtools view command is the most versatile tool in the samtools package. It’s main function, not surprisingly, is to allow you to convert the binary (i.e., easy for the computer to read and process) alignments in the BAM file view to text-based SAM alignments that are easy for humans to read and process.
Is there a way to extract CHRY read from SAMtools?
This isn’t really an answer to the original question. Plus if you want to extract chrY reads you only need a single command: This is true but still requires a sorted and indexed bam file. From the samtools manual: Use of region specifications requires a coordinate-sorted and indexed input file (in BAM or CRAM format).
How to extract reads corresponding to a specific chromosome from Bam?
It is rather easy to extract the reads corresponding to a specific chromosome from a BAM file using SAMtools. First we create the index file (BAI) for the BAM file with the following command: The previous command will generate the file Then we extract the data for specific region, for example chromosome 20.
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.
