On Sat, Jul 24, 2021 at 02:10:42AM +0800, Ching Ching WEE wrote: > I use the same bam file for both samtools mpileup (text pileup output) and > weeSAM (visualization) analysis. However, I found out the coverage is not > the same. For instance, weeSAM showed super high coverage,~116,000X, > between region 10,045-10,084 due to AT repeats as shown in the image here > but it is not detected in samtools mpileup. The same region only showed > ~3,000X read coverage in samtools mpileup. Any reason for such differences?
Yes. Take a look at the usage help for samtools mpileup, or better still the manual pages. Some key options which restrict depth and/or filter reads: -d, --max-depth INT max per-file depth; avoids excessive memory usage [8000] -A, --count-orphans do not discard anomalous read pairs -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13] Regards, 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. _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
