Single Nucleotide Variants Analysis

Raw Data

Input format and experiment type: Fastq, single-end

This file is a subset of public available sample LB901 from Doménech E, Gómez-López G, Gzlez-Peña D, López M, Herreros B, et al. (2012) New Mutations in Chronic Lymphocytic Leukemia Identified by Target Enrichment and Deep Sequencing. PLoS ONE 2012 7(6): e38158. doi:10.1371/journal.pone.0038158.

  • Reads number: 6326241
  • Reads length: 42

Steps

  1. Use RUbioSeq's LiveDVD or Download source code and install manually all programs and prerequisites for variant calling analysis especified in RUbioSeq's manual. Most of RUbioSeq's required programs can be downloaded here. Note: If you want to execute the quickTest with RubioSeq+GUI, follow the manual to launch and configure the graphical interface. Note: If you want to execute the quickTest with RubioSeq+GUI, follow the manual to launch and configure the graphical interface
  2. Download SNVs test data.
  3. Open a terminal

Decompress

cd YOUR_TEST_PATH
tar xvfz VariantTestData.tgz
cd VariantTestData/reference

Execute BWA indexing:

YOUR_BWA_PATH/bwa index -a bwtsw hg19.chr20.fa

Execute BFAST+BWA indexing:

YOUR_BFAST+BWA_PATH/bfast fasta2brg -f hg19.chr20.fa -A 0
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111111111111111111111" -w 14 -i 1
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111110111011101010010101101111" -w 14 -i 2
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1011110101101001011000011010001111111" -w 14 -i 3
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "10111001101001100100111101010001011111" -w 14 -i 4
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11111011011101111011111111" -w 14 -i 5
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111111100101001000101111101110111" -w 14 -i 6
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11110101110010100010101101010111111" -w 14 -i 7
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111101101011011001100000101101001011101" -w 14 -i 8
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111011010001000110101100101100110100111" -w 14 -i 9
YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111010010110110101110010110111011" -w 14 -i 10

Configure experiment XML file:

YOUR_TEST_PATH/VariantTestData/experimentTest.xml
You only need to configure the filenames paths to your corresponding directory.
You can modify the file using a text editor or RubioSeq+GUI

Configure programs XML file located at:

INSTALLATION_PATH/RUbioSeq_v3.2.1/variantCalling/config/snv/configProgramPaths.xml.
You can modify the file using a text editor or RubioSeq+GUI

RUN RUbioSeq:

Console execution
PathToRUbioSeq/RUbioSeq.pl --config YOUR_TEST_PATH/VariantTestData/experimentTest.xml
GUI execution
Click "Execute experiment" button, select the file and run. See for further information
Please read the manual to locate and understand the output files

Results

Final results with VEP annotations are available at PROJECT_DIRECTORY/SRR397777/calling/*.cleanNOTPASS.merged.