Getting Started
Installation
The latest version of SNVer is available here: SNVer Download, then unzip:
tar zxvf SNVer-x.x.x.tar.gz
Prepare a reference for testing
The toy data are generated from a real dataset from chrX.
So download chrX from UCSC,
wget http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/chrX.fa.gz then unzip it for the following testing:
gunzip chrX.fa.gz
Test for pooled sequencing data
Run the following command:
java -jar SNVerPool.jar -i test/bam/ -c test/test.ini
-r chrX.fa -l test/target.bed -o test_pool -t 0If successful, you should see the following:
Ready for Pool Pileup... Input Bam Directory is : test/bam/ Output Result File is : test_pool.raw.vcf test1:HAPLOIDS[2]MQ[17]BQ[30] test2:HAPLOIDS[2]MQ[20]BQ[20] The p-value cutoff (method: bonferroni=0.05) is 1.1148272017837236E-5 Filtered Output Result File is : test_pool.filter.vcf Time usage is 5 seconds Done!
Then you will get a list of p values for each loci in VCF 4.0 format, see more details about output in Manual.
Test for individual sequencing data
Run the following command:
java -jar SNVerIndividual.jar -i test/bam/test1.bam -o test_individual
-r chrX.fa -l test/target.bed If successful, you should see the following:
Ready for Pileup... Input Bam File is : test/bam/test1.bam Output Result File is : test_individual.raw.vcf The p-value cutoff (method: bonferroni=0.05) is 1.1606313834726092E-5 Filtered Output Result File is : test_individual.filter.vcf Time usage is 4 seconds Done!
Also see more details about output in Manual.