CompareBams4

##Motivation

Compare two BAM files. Print a tab-delimited report

##Compilation

Requirements / Dependencies

java compiler SDK 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make >= 3.81
curl/wget
git
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html (tested with "libxml 20706, libxslt 10126 and libexslt 815")

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make cmpbams4

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by adding standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make cmpbams4 standalone=yes

The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some definitions.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/cmpbams4.jar  [options] (stdin|file)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout.
-c|--chain (VALUE) Lift Over file from bam1 to bam2. Optional
-m|--mismatch (VALUE) Default Lift Over mismatch. negative=use default Default value : "-1".
-novalidchain|--novalidchain Disable Lift Over chain validation Default value : "false".
-st|--samtools Data was sorted using samtools sort -n algorithm (!= picard) see https://github.com/samtools/hts-specs/issues/5 Default value : "false".
-h|--help print help
-version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/cmpbams/CompareBams4.java

Example

The following Makefile compare the bam for hg19 and hg38 on chr22 and 21



include ../../config/config.mk

CHROMS=21 22
OUTDIR=tmp

define run
${OUTDIR}/$(1).bam : ${OUTDIR}/$(1).fa.bwt R1.fastq.gz R1.fastq.gz
	${bwa.exe} mem -M   -R '@RG\tID:SAMPLE\tLB:SAMPLE\tSM:SAMPLE\tPL:illumina\tCN:Nantes' ${OUTDIR}/$(1).fa $$(word 2,$$^) $$(word 3,$$^) |  ${samtools.exe} view -b -u -S -F4 - | ${samtools.exe} sort -n -o $$@ -T ${OUTDIR}/$(1)_tmp -

${OUTDIR}/$(1).fa.bwt : ${OUTDIR}/$(1).fa
	${bwa.exe} index $$<

${OUTDIR}/$(1).dict : ${OUTDIR}/$(1).fa
	${java.exe} -jar $(picard.jar) CreateSequenceDictionary R=$$< O=$$@

${OUTDIR}/$(1).fa.fai : ${OUTDIR}/$(1).fa
	${samtools.exe} faidx $$<
	
${OUTDIR}/$(1).fa : 
	mkdir -p $$(dir $$@) && rm -f $$@
	$$(foreach C,${CHROMS}, curl "http://hgdownload.cse.ucsc.edu/goldenPath/$(1)/chromosomes/chr$${C}.fa.gz" | gunzip -c >> $$@;)

endef

all:  ${OUTDIR}/diff.txt 

${OUTDIR}/diff.txt : ${OUTDIR}/hg19.bam ${OUTDIR}/hg38.bam ${OUTDIR}/hg19ToHg38.over.chain ${OUTDIR}/hg19.dict ${OUTDIR}/hg38.dict
	mkdir -p $(dir $@) &&  $(call run_jvarkit,cmpbams4) --novalidchain -st -c $(word 3,$^) $(word 1,$^)  $(word 2,$^) > $@

${OUTDIR}/hg19ToHg38.over.chain :
	mkdir -p $(dir $@) && curl "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz" | gunzip -c > $@

$(eval $(call run,hg19))
$(eval $(call run,hg38))

Output

onlyIn	liftover	compareContig	shift	diffCigarOperations	diffNM	diffFlags	diffChroms	Count
BOTH	SameChrom	DiscordantContig	.	-1	0	147/163	chr22/chr21	2
BOTH	SameChrom	SameContig	Gt100	3	15	83/83	chr22/chr22	1
BOTH	SameChrom	DiscordantContig	.	3	5	147/129	chr21/chr22	1
BOTH	SameChrom	SameContig	Gt100	-1	1	163/163	chr22/chr22	22
BOTH	SameChrom	DiscordantContig	.	0	1	83/99	chr21/chr22	32
BOTH	SameChrom	SameContig	Gt100	0	2	99/99	chr21/chr21	22
BOTH	SameChrom	DiscordantContig	.	2	6	81/65	chr22/chr21	1
BOTH	SameChrom	SameContig	Gt100	0	0	185/137	chr22/chr22	20
BOTH	SameChrom	SameContig	Zero	0	0	177/177	chr22/chr22	1417
(...)