EBCall specifications

Information


Unique identifier OMICS_00084
Name EBCall
Alternative name Empirical Baysian mutation Calling
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Target tumor sample, target normal sample and list of normal reference samples.
Input format BAM
Output data The position of the candidate mutation, the reference base for that position, he alternated sequence for the mutation candidate, sequencing depth for positive strand or both tumor and normal samples, the mismatch rates computed in the tumor and normal samples, the ratio of variant reads aligned to positive strand for the tumor and normal samples, sequencing depths for that position for the tumor and normal samples, he number of supporting variant read in the tumor and normal samples p-value, the minus logarithm of p-value of the EBCall for positive and negative strand, respectively, he minus logarithm of the p-value by Fisher's exact test and the estimated parameter values of Beta-Binominal sequencing model for that variant.
Operating system Unix/Linux
Programming languages C++, Perl, R, Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements samtools, The VGAM package for R
Maintained Yes

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Maintainers


  • person_outline Satoru Miyano <>
  • person_outline Yuichi Shiraishi <>
  • person_outline Seishi Ogawa <>
  • person_outline EBCall Team <>

Publication for Empirical Baysian mutation Calling

EBCall institution(s)
Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan; Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Hematology/Oncology, Gunma Children’s Medical Center, Gunma, Japan

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