Quick Guide to use LQSR program
All sources and binaries are on http://www.hgc.jp/~ig/LQSR/sample/LQSR_ver1.tgz
Step 1: First you need to create pileup file from the given sam or bam file. To create pileup file you can use the de facto standard software samtools.
> samtools mpileup ${input.bam} ${output.pileup}
(Note) The pileup format is not supported in the latest samtools need to download older version.
Step 2: Create a re-calibration table from a learning pileup file.
> java -Xmx1024M -jar LQSRCreateTable.jar -i ${input.pileup} -o ${output.re-calibration.table.prefix} -l 'length of short read length'
(Note) The required memory size might depend on the running environment.
(Note) Three files ${output.re-calibration.table.prefix}.aln3, ${output.re-calibration.table.prefix}.aln3.data and ${output.re-calibration.table.prefix}.aln3.norm are created.
Step 3: Re-calibrate the target sam or bam file from the re-calibration table in Step 2.
> java -Xmx1024M -jar LQSRRecalibrate.jar -t ${input.re-calibration.table.prefix} -i ${target.sam.or.bam.file.to.recalibrate} -o ${output.sam} -l 'length of reads'
(Note) The required memory size might depend on the running environment.
Alignment and summarized (pileup) result of DRX001619 human data in DDBJ can be obtained from
Data1) Aligned result of half DRX001619 dataset to hg19 reference genome using BWA.
http://www.hgc.jp/~ig/LQSR/sample/DRX001619_learning.sorted.bam
Data2) Pipeup data generated from 1.
http://www.hgc.jp/~ig/LQSR/sample/DRX001619_learning.sorted.pileup
Data3) Aligned result of remnant half DRX001619 dataset to hg19 reference genome using BWA for quality recalibration test.
http://www.hgc.jp/~ig/LQSR/sample/DRX001619_target.sorted.sam
Data2 can be created from Data1 by using the operation in Step 2.
Data3 can be used as an example of ${target.sam.or.bam.file.to.recalibrate}.
All packed data is http://www.hgc.jp/~ig/LQSR/sample/LQSR/sample.tgz
Any question please contact to Masao Nagasaki nagasaki@megabank.tohoku.ac.jp and Ohtsuki Tomohiko tomo_o@hgc.jp