What is samtools index?
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 a Bai file BAM?
A bai file isn’t an indexed form of a bam – it’s a companion to your bam that contains the index. A bam file is a binary blob that stores all of your aligned sequence data. You can view what’s in the bam file using “samtools view bamfile. bam | less”. Bam files can also have a companion file, called an index file.
How do I convert a BAM file to IGV?
In IGV, select File > Load from URL … A window will pop up and ask you to give the correct URL for the file you want to view. Paste in the URL and the file will be downloaded. From the file extension, IGV will automatically treat the information in the file accordingly.
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 is SAM and BAM file?
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.
Can IGV open BAM files?
File Formats Aligned reads from sequencing can be loaded into IGV in the BAM format, SAM format, or CRAM format.
What are SAM and BAM files?
SAM vs. BAM. In bioinformatics, alignment data for large numbers of aligned reads are often output as a sequence alignment and map (SAM) or binary alignment and map (BAM) file. Alignment is a common step in many bioinformatics workflows involving nucleic acid sequencing.
Are BAM files smaller than SAM?
For almost any application that requires SAM input, this can be created on the fly from a BAM file (using ‘samtools view reads. bam |’). BAM files take up much less space than SAM files. For archiving purposes, keep only the BAM file.
How much memory does SAMtools sort use?
While running SAMtools, we provisioned only 45 Gb (1.5 Gb for each of the 30 threads) so one should only specify 80-90% of available memory to SAMtools. Sambamba used close to the 45 Gb memory we specified for the first 5 minutes before dropping the memory used to 2Gb.
What does SAMtools Flagstat do?
DESCRIPTION. Does a full pass through the input file to calculate and print statistics to stdout. Provides counts for each of 13 categories based primarily on bit flags in the FLAG field. Information on the meaning of the flags is given in the SAM specification document .
What does red mean in IGV?
In IGV such an event might look like the following. Reads that are colored red have larger than expected inferred sizes, and therefore indicate possible deletions.