qMule AlignerCompare

This mode of the qMule tool will take 2 BAMs (sorted on QNAME) and will compare BAM records. It is intended for use in cases where we want to compare 2 different aligners or the same aligner run with different options. The tool creates 3 output BAMs:

• all records that are identical
• records from BAM1 that don't match BAM2
• records from BAM2 that don't match BAM1

It is assumed that the 2 input BAM files were created from the same FASTQ files so all of the reads in BAM 1 must also appear in BAM 2 although there may be more than one record per read which allows for secondary alignments to be present. The input BAMs are required to be sorted by QNAME not POS so that all alignments for a given read are adjacent. Only reads that are unaligned or primary alignments will be compared so secondary alignments are invisible to AlignerCompare unless you choose "compareAll" as [option].

We treat two alignments as the same if these fields are identical:

• QNAME - query template name (read ID)
• FLAG - bitwise FLAG
• RNAME - reference sequence name (usually the chromosome or config)
• POS - 1-based leftmost alignment position
• alignment end position
• MAPQ - mapping quality
• CIGAR - CIGAR string
• MD field - optional field that provides a representation of the base-by-base alignment.

For the purposes of the optional MD field, the reads are considered to match if both align with the same MD string or both are missing the MD field so both or neither of the input BAMs should have the MD field.

Usage:

usage: qmule org.qcmg.qmule.AlignerCompare -i <bam1> -i <bam2> -o <output prefix with full path> [options]
Option                                  Description                            
------                                  -----------                            
--compareAll            Without this option, this comparison will discard all non primary alignments, such as secondary,  supplementary alignments.            
-h, --help            Shows this help message.               
-i, --input <input>    Specifies an input file.               
-o, --output <output>    Specifies output file prefix with full path here                            
-v, --version        Print version info.                 

Here, please use option "compareAll" if you don't want to discard all non-primary alignment (secondary and supplementary alignments). This tool will splits all alignment into three output BAMs as shown on below example:

java -cp qmule-0.1pre.jar org.qcmg.qmule.AlignerCompare -i mem.queryname.bam -i back.queryname.bam -o /output/prefix

• output1: /output/prefix.identical.bam will stores all alignments which are same from both input BAMs
• output2: /output/prefix.different.memSort.bam will stores all primary alignments which is from first BAM but different to second BAM
• output3: /output/prefix.different.backSort.bam will stores all primary alignments which is from second BAM but different to first BAM
• with option "compareAll", the non-primary alignment will be keep in output2 or output3, otherwise these alignments will be discarded by default.
• the name of output2 and output 3 will be /output/prefix.different.first.bam and /output/prefix.different.second.bam if both inputs with same name but from different location.
• A log file named /output/prefix.log will be created in this case, see below example:

A log file named /output/path/<prefix>.log will be created. It will look like:

12:13:28.986 [main] INFO org.qcmg.qmule.AlignerCompare - input BAM1: /input/mem.queryname.bam
12:13:28.987 [main] INFO org.qcmg.qmule.AlignerCompare - input BAM2: /input/back.queryname.bam
12:13:28.987 [main] INFO org.qcmg.qmule.AlignerCompare - discard secondary or supplementary alignments: true
12:13:29.031 [main] INFO org.qcmg.qmule.AlignerCompare - output of identical reads: /output/prefix.identical.bam
12:13:29.031 [main] INFO org.qcmg.qmule.AlignerCompare - output of unique reads from BAM1: /output/prefix.different.mem.queryname.bam
12:13:29.032 [main] INFO org.qcmg.qmule.AlignerCompare - output of unique reads from BAM2: /output/prefix.different.back.queryname.bam
14:09:06.193 [main] INFO org.qcmg.qmule.AlignerCompare - There are 100411877 reads with 244684085 alignments from BAM1
14:09:06.219 [main] INFO org.qcmg.qmule.AlignerCompare - There are 100411877 reads with 200823754 alignments from BAM2
14:09:06.220 [main] INFO org.qcmg.qmule.AlignerCompare - There are 146425081 alignments are identical from both BAM
14:09:06.220 [main] INFO org.qcmg.qmule.AlignerCompare - Different alignments from BAM1 are 54398673, from BAM2 are 54398673
14:09:06.221 [main] INFO org.qcmg.qmule.AlignerCompare - discard 43426907 secondary alignments and 433424 supplementary alignments from BAM1
14:09:06.229 [main] INFO org.qcmg.qmule.AlignerCompare - discard 0 secondary alignments and 0 supplementary alignments from BAM2
14:09:07.231 [main] INFO org.qcmg.qmule.AlignerCompare - It took 1 hours, 55 seconds to perform the comparison
14:09:07.231 [main] EXEC org.qcmg.qmule.AlignerCompare - StopTime 2014-03-12 14:09:07
14:09:07.232 [main] EXEC org.qcmg.qmule.AlignerCompare - ExitStatus 0
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