Hello all I’ve recently started using the HTSJDK to access BAM files in for my current project, as part of this I need to extract the number of reads covering a specific site.
As such is there a specific function in the htsjdk to retrieve the number of reads/alignments that cover a specific position i.e. chr2:10,000? Or is this something that requires some coding, say iterating through a query from a SamReader? If so does any one have any recommendations/code snippets for the most efficient way to do this? As determining read depths for the bases in a few thousand 1kb windows seems like it would be a little slow if I need to do a query for each position i.e. chr2:10,000-10,001 in each 1kb window and then iterate through the returned sam records for each site. Thanks Chad Harland University of Liege - Belgium ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
