Nucleotide Diversity Calculations

Overview

This program estimates the nucleotide diversity of genomic sequences.

Usage

Step 1 - BAM Files Conversion

Convert the BAM files using Samtools.

samtools view -h -G69 to.convert.bam | samtools view -h -G133 > file.bam

For every sample, generate a strandcount.csv from the BAM file.

java -cp /your-path-to/HAROLD/lib/htsjdk-unspecified-SNAPSHOT.jar:
/Your-path-to/HAROLD/lib/picocli-4.1.2.jar:
/Your-path-to/HAROLD/lib/pal-1.5.1.jar:
/Your-path-to/HAROLD/lib/cache2k-all-1.0.2.Final.jar:
/Your-path-to/HAROLD/lib/commons-math3-3.6.1.jar:
/Your-path-to/HAROLD/jar/MakeReadCount.jar makereadcount.MakeReadCount file.bam

Step 2 - Diversity Estimations

java -jar MultiFileDiversity.jar -dataFileList sample.txt > diversity.txt

Getting help

If you have any questions, please feel free to contact Juanita Pang or Richard Goldstein.