Hi, We are trying to make use of the HS_PENALTY_30X calculation to estimate if it is worth sequencing a few of our libraries deeper. We ran into one case that we don't fully understand:
For one sample the HS_PENALTY_30X value is 27.9296 and the PCT_TARGET_BASES_30X value is already at 0.823152. Our PF_ALIGNED_BASES is already at 1,864,338,086. When we run the calculation from the metrics description, it tells us that we need to sequence until PF_ALIGNED_BASES = 2,094,720,000 to get 80% of targets over 30X. Basically, the metric is telling us we need 230,381,914 additional PF_ALIGNED_BASES to get to 80% over PCT_TARGET_BASES_30X even though we already hit that mark. Is this just the inherent fuzziness in how this metric is generated? Or are we misunderstanding something? Thanks, Matt -- Matthew Ducar Group Leader Clinical Bioinformatics Center for Cancer Genome Discovery (CCGD) Dana Farber Cancer Institute, Dana 840B 44 Binney St. Boston, MA 02115 Tel: 617 582-9704 Mailing address: Dana Farber Cancer Institute 450 Brookline Ave, Boston, MA 02215 matthewd_du...@dfci.harvard.edu www.cancergenomediscovery.com The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
