On Fri, Jul 13, 2018 at 06:44:30PM +1000, Jing meng wrote: > I run samtools mpileup and set the -d 100 (max per-file depth), and that is > the ouput information: > > [mpileup] 1 samples in 2 input files > <mpileup> Set max per-file depth to 8000 > > Why the output (max per-file depth to 8000) is different from What I set > (max per-file depth to 100)?
This has been fixed in develop and will be in an official release shortly. > Also, is the per-file depth the per-site depth? It's used to set the maximum depth of reads starting at each site, per input file. > I set the -d to be 100. Why I still get some records in the pileup file > whose depth is larger than 100 at the genomic site? The depth limit isn't really a limit, but a hint used to prevent slow downs when getting to extremely deep regions. Specifically it limits the number of reads *starting* at each site, so -d 100 will mean no more than 100 reads starting at position X, but another 100 at at position X+1 will be permitted. Assuming more than 1bp long reads that then gives depth 200. The reason for this logic is if we blocked reads at X to X+L (assuming fixed length L) then we'd get a huge drop in depth immediately following this, potentially to zero. The problem here is the wording of the option which implies a hard limit rather than as a filtering option for efficiency purposes. James -- James Bonfield (j...@sanger.ac.uk) The Sanger Institute, Hinxton, Cambs, CB10 1SA -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
