CmpBamAndBuild

##Motivation

Compare two BAM files mapped on two different builds. Requires a liftover chain file.

##Compilation

See also Compilation.

$  ant cmpbamsandbuild

##Synopsis

$ java -jar distcmpbamsandbuild.jar [options] -c A_to_B.chain bamA.bam bamB.bam

##Options

Option	Description
-c (chain file)	Lift Over file from bam1 to bam2. REQUIRED
-d (dist)	distance tolerance between two alignments.
-r (region)	restrict to that region chr:start-end
-n (int)	When writing data that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort a SAM file, and increases the amount of RAM needed. Optional.
-T (dir)	Add a temporary directory. Optional.
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

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

##Example The following Makefile compares two BAMs mapped on hg19 and hg38.

BWA=bwa
SAMTOOLS=samtools
.PHONY:all

all: file.diff

file.diff.gz : hg19ToHg38.over.chain hg19.bam hg38.bam
	java -jar jvarkit-git/dist/cmpbamsandbuild.jar -d 20 \
	    -c hg19ToHg38.over.chain hg19.bam hg38.bam | gzip --best > $@

hg38.bam:file1.fastq.gz file2.fastq.gz
	${BWA} mem  index-bwa-0.7.6a/hg38.fa $^ |\
		${SAMTOOLS} view -Sb - |\
		${SAMTOOLS}  sort - hg38 && \
		${SAMTOOLS} index hg38.bam
		
hg19.bam: file1.fastq.gz file2.fastq.gz
		${BWA} mem index-bwa-0.7.6a/hg19.fa $^ |\
		${SAMTOOLS} view -Sb - |\
		${SAMTOOLS}  sort - hg19 && \
		${SAMTOOLS} index hg19.bam


hg19ToHg38.over.chain:
	curl -o $@.gz http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/$@.gz && gunzip -f $@.gz

file.diff :

#READ-Name	COMPARE	hg19.bam	hg38.bam
HWI-1KL149:18:C0RNBACXX:3:1101:10375:80749/2	NE	chrMasked:581319279->chrMasked:581415967	chrMasked:581703411
HWI-1KL149:18:C0RNBACXX:3:1101:10394:60111/1	NE	chrMasked:581319428->chrMasked:581416116	chrMasked:581703560
HWI-1KL149:18:C0RNBACXX:3:1101:10394:60111/2	NE	chrMasked:581319428->chrMasked:581416116	chrMasked:581703560
HWI-1KL149:18:C0RNBACXX:3:1101:10413:69955/1	NE	chrMasked:581318674->chrMasked:581415362	chrMasked:581702806
HWI-1KL149:18:C0RNBACXX:3:1101:10413:69955/2	NE	chrMasked:581318707->chrMasked:581415395	chrMasked:581702839
HWI-1KL149:18:C0RNBACXX:3:1101:10484:89477/1	NE	chrMasked:581319428->chrMasked:581416116	chrMasked:581703560
HWI-1KL149:18:C0RNBACXX:3:1101:10484:89477/2	NE	chrMasked:581319428->chrMasked:581416116	chrMasked:581703560
HWI-1KL149:18:C0RNBACXX:3:1101:10527:3241/1	NE	chrMasked:581319279->chrMasked:581415967	chrMasked:581703411
HWI-1KL149:18:C0RNBACXX:3:1101:10527:3241/2	NE	chrMasked:581319279->chrMasked:581415967	chrMasked:581703411
HWI-1KL149:18:C0RNBACXX:3:1101:10580:13030/1	NE	chrMasked:581319331->chrMasked:581416019	chrMasked:581703463
HWI-1KL149:18:C0RNBACXX:3:1101:10580:13030/2	NE	chrMasked:581319331->chrMasked:581416019	chrMasked:581703463
HWI-1KL149:18:C0RNBACXX:3:1101:10618:51813/1	EQ	chrMasked:581318674->chrMasked:581415362	chrMasked:581415362
HWI-1KL149:18:C0RNBACXX:3:1101:10618:51813/2	NE	chrMasked:581318707->chrMasked:581415395	chrMasked:581702839
HWI-1KL149:18:C0RNBACXX:3:1101:10803:23593/1	NE	chrMasked:581319091->chrMasked:581415779	chrMasked:581703223
HWI-1KL149:18:C0RNBACXX:3:1101:10803:23593/2	NE	chrMasked:581319091->chrMasked:581415779	chrMasked:581703223
HWI-1KL149:18:C0RNBACXX:3:1101:11290:76217/1	EQ	chrMasked:581318674->chrMasked:581415362	chrMasked:581415362
HWI-1KL149:18:C0RNBACXX:3:1101:11290:76217/2	NE	chrMasked:581318707->chrMasked:581415395	chrMasked:581702839
HWI-1KL149:18:C0RNBACXX:3:1101:11307:71853/1	NE	chrMasked:581319254->chrMasked:581415942	chrMasked:581703386
HWI-1KL149:18:C0RNBACXX:3:1101:11307:71853/2	NE	chrMasked:581319258->chrMasked:581415946	chrMasked:581703390
HWI-1KL149:18:C0RNBACXX:3:1101:11359:100655/1	EQ	chrMasked:581318923->chrMasked:581415611	chrMasked:581415611
HWI-1KL149:18:C0RNBACXX:3:1101:11359:100655/2	EQ	chrMasked:581318923->chrMasked:581415611	chrMasked:581415611
HWI-1KL149:18:C0RNBACXX:3:1101:11467:8793/1	NE	chrMasked:581319428->chrMasked:581416116	chrMasked:581703560
HWI-1KL149:18:C0RNBACXX:3:1101:11467:8793/2	NE	chrMasked:581319428->chrMasked:581416116	chrMasked:581703560
HWI-1KL149:18:C0RNBACXX:3:1101:11560:69825/1	EQ	chrMasked:581319331->chrMasked:581416019	chrMasked:581416019
HWI-1KL149:18:C0RNBACXX:3:1101:11560:69825/2	EQ	chrMasked:581319335->chrMasked:581416023	chrMasked:581416023

##See also

• CmpBams

##History

• 2014: Creation