This tool is designed to act as a pre-processor for copy number analysis tools. It reads one or more BAM files and outputs the read counts within a given window-size to a VCF-like plain text file.
qCNV requires java 8 and (ideally) a multi-core machine. qCNV is threaded for increased execution speed and is relatively memory efficient at approximately 2GB for a single thread although the memory use scales linearly with thread count so using large numbers of threads requires large amounts of memory. To install:
You should see jar files for qbamfilter and its dependencies:
> tar xjvf qcnv-0.3.tar.bz2 x antlr-3.2.jar x commons-cli-1.2.jar x htsjdk-1.140.jar x jopt-simple-4.6.jar x picard-lib.jar x qbamfilter-1.2.jar x qcnv-0.3pre.jar x qcommon-0.3.jar x qpicard-1.1.jar x trove-3.1a1.jar
usage: java -jar qcnv-0.3pre.jar -i <BAM> --id <sample id> -o <output> --log <log file> [options] Option Description ------ ----------- -h,--help Shows this help message. -v,--version Print version info. -i,--input <input BAM> specify the input BAM file with full path --id <sample id> specify the sample id here, which will be used as column name showing on output header. -o,--output <count file> Specifies the output file. --log <log file> specify the log file, by default it will be <output file>.log --thread <thread number> (Optional) specify the thread number (the number of paralleled query). by default we set it to 2 -w,--window_size <window size> (Optional) specify the window size here. by default we set it to 10000. -q,--query <query string> (Optional) The query string for selecting reads for cnv counts.
Example
java -jar -Xms40g -Xmx40g qcnv-0.3pre.jar \ -i $tumourBAM --id tumour \ -i $normalBAM --id normal \ -i $metastasisBAM --id metastasis \ -o $countFile -w 10000 \ -q "and (RNAME =~ chr*, cigar_M >= 100)" \ --log $logfile --thread 16
This example inputs three BAMs with labels "tumour", "normal" and "metastasis". These labels will appear in the output file as the column headers. All related counts in each window will be shown as below:
#CHROM ID START END FORMAT tumour normal metastasis chr1 1_10000 1 10000 DP 0 0 0 chr1 2_10000 10001 20000 DP 412 0 2 chr1 3_10000 20001 30000 DP 300 0 1 chr1 4_10000 30001 40000 DP 200 159 109 ...