![]() 2.2 I want to call SNPs and short indels.1.3 CIGAR is `50M', but I see mismatches in the alignment.1.2 How unaligned reads are stored in SAM?.1.1 How can I get alignments in the SAM/BAM format?.You can check out the most recent source code from the github project page with: The source code releases are available from the download page. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory.Is simple enough to be easily generated by alignment programs or converted from existing alignment formats.Is flexible enough to store all the alignment information generated by various alignment programs.SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
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