I'm currently experimenting with split-reads alignment to detect deletions in WGS data and I'm wondering whether samtools mpileup combined with bcftools is able to call larger deletions (typically several hundred bases) as opposed to just small indels when presented with appropriately aligned reads. From a first test with samtools 0.1.19 and engineered bam data simulating a 1.4 kb deletion the answer seems to be no, but I'd be grateful for any help or explanation why it can't work.
Thanks a lot, Wolfgang ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
