p-dindel
shabbir5@vt.edu
Author: Mohammad Shabbir Hasan PhD Student, Department of Computer Science Virginia Tech, Blacksburg, VA 24060, USA. E-mail:System Requirement
-GCC and Python. -P-Dindel has been tested with GCC version 4.6.3 and Python version 2.7.3 in the Ubuntu 12.04 LTS operating system.
Compiling
-To compile p-dindel.cpp use the following command g++ p-dindel.cpp -std=c++0x -lpthread -lrt -o p-dindel
-To compile p-dindel_pooled.cpp use the following command g++ p-dindel_pooled.cpp -std=c++0x -lpthread -lrt -o p-dindel_pooled
Execution of the program
-To run P-Dindel for diploid sample, you need to use the following command: ./p-dindel -i input_bam_file_name -o output_file_name -r reference_fasta_file_name
-To run P-Dindel for pooled samples, you need to use the following command: ./p-dindel_pooled -i input.txt -o output_file_name -r reference_fasta_file_name
Here input.txt contains the list of bam file for each sample in the pool (1 bam file in each line).