Tag: Swap

verifyBamID 1.1.3 – Identify Contamination of Sample Swap in Sequence data

verifyBamID 1.1.3

:: DESCRIPTION

verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples

::DEVELOPER

Abecasis Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
:: DOWNLOAD

 verifyBamID

:: MORE INFORMATION

Citation

G. Jun, M. Flickinger, K. N. Hetrick, Kurt, J. M. Romm, K. F. Doheny, G. Abecasis, M. Boehnke,and H. M. Kang,
Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data,
Am J Hum Genet. 2012 Nov 2;91(5):839-48. doi: 10.1016/j.ajhg.2012.09.004. (volume 91 issue 5 pp.839 – 848)

SWAP 0.9 – Analyse Genetic Parameters in Half Sib Families

SWAP 0.9

:: DESCRIPTION

SWAP was developed to calculate the genetic diversity (AR, Hs, Ht) of and the genetic differentiation (Gst, D, Dest) among different half-sib families (embryos, respective pollen clouds) and within and among two different generations. Calculations are based on the father alleles. In the case that the embryo has the same genotype as the mother, it is not possible to decide which allele comes from the mother and which one comes from the father. In such ambiguous cases, the genetic parameters are measured via a Jackknifing-procedure. In addition, SWAP calculates all genetic parameters within and among several adult populations.

::DEVELOPER

Dr. Ronald Bialozyt

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  SWAP

:: MORE INFORMATION