3/7/2023 0 Comments View sam file linux![]() One-based index: Start and end positions are identified using a one-based index. For convenience, IGV equates chromosome numbers and names of the form chr# (e.g., 1 and chr1 are equivalent). SAI index is an IGV format, and it does not work with samtools or any other application.Ĭhromosome names: Chromosome names must be consistent between the selected reference genome and the SAM/BAM data files. SAM files can be sorted and indexed using igvtools. The GenePattern module for sorting and indexing is Picard.SortSam. Multiple tools are available for sorting and indexing BAM files, including igvtools, the samtools package, and in GenePattern. The index files must have the same base file name and must reside in the same directory as the file that it indexes.įor example, the index file for test-xyz.bam would be named or test-xyz.bai. A SAM index filename is created by appending. Specifically, a BAM index file should be named by appending. Indexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Starting with IGV 2.0.11, IUPAC ambiguity codes in BAM files are supported. īAM, rather than SAM, is the recommended format for IGV. These formats are described on the SAM Tools web site. A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data. To load a set of BAM files merged into a single track see Merged BAM File.Ī BAM file (.bam) is the binary version of a SAM file. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |