CompareBams

Last commit

Compare two or more BAM files

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar cmpbams  [options] Files

Usage: cmpbams [options] Files
  Options:
    -c, --cigar
      use cigar String for comparaison
      Default: false
    -d, --distance
      distance tolerance between two alignments
      Default: 10
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -Q, --mapq
      min MAPQ
      Default: 0
    --maxRecordsInRam
      When writing  files 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 file, and increases 
      the amount of RAM needed
      Default: 50000
    --no-filter
      Do not filter the reads. Default is to ignore secondary or supplementary 
      alignments. 
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
    -R, --reference
      For CRAM. Indexed fasta Reference file. This file must be indexed with 
      samtools faidx and with picard/gatk CreateSequenceDictionary or samtools 
      dict 
    -r, --region
      An interval as the following syntax : "chrom:start-end". Some jvarkit 
      programs also allow the following syntax : "chrom:middle+extend"  or 
      "chrom:start-end+extend" or "chrom:start-end+extend-percent%".A program 
      might use a Reference sequence to fix the chromosome name (e.g: 1->chr1)
      Default: <empty string>
    -F, --sam
      use sam flag for comparaison
      Default: false
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --version
      print version and exit

Keywords

sam
bam
compare

Creation Date

20130506

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/cmpbams/CompareBams.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/cmpbams/CompareBamsTest.java

Contribute

Issue Tracker: http://github.com/lindenb/jvarkit/issues
Source Code: http://github.com/lindenb/jvarkit

License

The project is licensed under the MIT license.

Citing

Should you cite cmpbams ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

Question was : "mapping with BWA produced a variation one year ago. We then mapped the same fastq with two different sets of parameters, but we cannot find the variant anymore. Has the mapping changed ?"

Extract the read names from the original BAM:

samtools view  file1.bam K01:2179-2179 |\
 cut -d '   ' -f 1  | sort | uniq > names.txt

Use [[SamGrep]] to retieve the reads in the 3 bams:

java -jar dist/samgrep.jar -f names.txt file1.bam &gt; tmp1.sam
java -jar dist/samgrep.jar -f names.txt file2.bam &gt; tmp2.sam
java -jar dist/samgrep.jar -f names.txt file3.bam &gt; tmp3.sam

Run CmpBams

$ java -jar dist/cmpbams.jar -F -C tmp1.sam tmp2.sam tmp3.sam

#READ-Name  tmp1.sam tmp2.sam|tmp1.sam tmp3.sam|tmp2.sam tmp3.sam   tmp1.sam    tmp2.sam    tmp3.sam
HWI-1KL149:20:C1CU7ACXX:1:1101:17626:32431/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:1101:17626:32431/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1102:16831:71728/1    EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1102:16831:71728/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1105:3309:27760/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1105:3309:27760/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1106:2914:12111/1 EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:1106:2914:12111/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1107:11589:17295/1    EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1107:11589:17295/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1110:14096:95943/1    EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1110:14096:95943/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1110:15369:59046/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1110:15369:59046/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1111:8599:97362/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1111:8599:97362/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:10490:30873/1    EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:10490:30873/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:12360:36316/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:12360:36316/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1113:4589:62685/1 EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:1113:4589:62685/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1115:7288:99676/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1115:7288:99676/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1116:8136:52921/1 EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1116:8136:52921/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:11809:66877/1    EQ|EQ|EQ    K01:2104=83/100M    K01:2104=83/100M    K01:2104=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:11809:66877/2    EQ|EQ|EQ    K01:2043=163/100M   K01:2043=163/100M   K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:18844:98575/1    EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1202:18844:98575/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1205:20782:28689/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1205:20782:28689/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1206:10108:83718/1    EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1206:10108:83718/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1212:17964:23344/1    EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1212:17964:23344/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1213:9111:56546/1 EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1213:9111:56546/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:4380:98965/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:4380:98965/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:4493:85995/1 EQ|NE|NE    K01:2143=83/36S36M3I25M K01:2143=83/36S36M3I25M K01:2107=83/72M3I25M
HWI-1KL149:20:C1CU7ACXX:1:1216:4493:85995/2 EQ|EQ|EQ    K01:2043=163/100M   K01:2043=163/100M   K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:8034:78319/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:1216:8034:78319/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:1316:14751:4679/1 EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:1316:14751:4679/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2102:4725:60173/1 EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2102:4725:60173/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2104:19271:24502/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2104:19271:24502/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2104:2016:81735/1 EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2104:2016:81735/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2110:4445:72697/1 EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2110:4445:72697/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2111:2256:47748/1 EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2111:2256:47748/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2115:12497:79931/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2115:12497:79931/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2115:17576:9737/1 EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2115:17576:9737/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2116:7977:30610/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2116:7977:30610/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2201:16984:100451/1   EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2201:16984:100451/2   EQ|EQ|EQ    K01:2059=163/87M13S K01:2059=163/87M13S K01:2059=163/87M13S
HWI-1KL149:20:C1CU7ACXX:1:2203:19912:68616/1    EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2203:19912:68616/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2204:13318:18341/1    EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2204:13318:18341/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:10726:12303/1    EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:10726:12303/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:11557:78671/1    EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2206:11557:78671/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2211:12806:63973/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2211:12806:63973/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:17602:62052/1    EQ|EQ|EQ    K01:2104=83/100M    K01:2104=83/100M    K01:2104=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:17602:62052/2    EQ|EQ|EQ    K01:2043=163/100M   K01:2043=163/100M   K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:19408:52552/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2212:19408:52552/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2303:8733:45438/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2303:8733:45438/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2304:9806:12935/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2304:9806:12935/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2305:12165:42334/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2305:12165:42334/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2305:2388:67842/1 EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2305:2388:67842/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:14199:91258/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:14199:91258/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:3121:93985/1 EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2307:3121:93985/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2309:13907:13532/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2309:13907:13532/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2309:20396:57002/1    EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:1:2309:20396:57002/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2312:11602:6630/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2312:11602:6630/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2313:11868:31327/1    EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2313:11868:31327/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2313:9555:94108/1 EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:1:2313:9555:94108/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:1:2315:19820:15046/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:1:2315:19820:15046/2    EQ|EQ|EQ    K01:2081=163/99M1S  K01:2081=163/99M1S  K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1101:18362:28315/1    EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1101:18362:28315/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:18846:45527/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:18846:45527/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:5659:65125/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1105:5659:65125/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1108:9609:39170/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1108:9609:39170/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1110:2262:8369/1  EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1110:2262:8369/2  EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1111:18496:5547/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1111:18496:5547/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:10132:23322/1    EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:10132:23322/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:7260:56414/1 EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1112:7260:56414/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1201:6906:82750/1 EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:2:1201:6906:82750/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1202:16231:100362/1   EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1202:16231:100362/2   EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1213:12574:89489/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:1213:12574:89489/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1214:20898:3105/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1214:20898:3105/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:```20:C1CU7ACXX:2:1214:7035:46585/1  EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1214:7035:46585/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1215:19107:31048/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1215:19107:31048/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1216:15500:73171/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:1216:15500:73171/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1216:6409:43952/1 EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1216:6409:43952/2 EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1301:16595:88662/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1301:16595:88662/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1306:12619:24138/1    EQ|NE|NE    K01:2143=83/36S36M3I25M K01:2143=83/36S36M3I25M K01:2107=83/72M3I25M
HWI-1KL149:20:C1CU7ACXX:2:1306:12619:24138/2    EQ|EQ|EQ    K01:2043=163/100M   K01:2043=163/100M   K01:2043=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1308:8618:21991/1 EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:2:1308:8618:21991/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1309:15540:69632/1    EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1309:15540:69632/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1314:9489:93274/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1314:9489:93274/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:1316:5692:99314/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:1316:5692:99314/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2108:14003:59876/1    EQ|EQ|EQ    K01:2136=83/44M3I53M    K01:2136=83/44M3I53M    K01:2136=83/44M3I53M
HWI-1KL149:20:C1CU7ACXX:2:2108:14003:59876/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2113:14713:81195/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2113:14713:81195/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2114:13002:89288/1    EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2114:13002:89288/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2201:11170:94334/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:2201:11170:94334/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2202:4380:42920/1 EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2202:4380:42920/2 EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:14141:87844/1    EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:14141:87844/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:15510:90052/1    EQ|EQ|EQ    K01:2122=83/57M3I23M1D17M   K01:2122=83/57M3I23M1D17M   K01:2122=83/57M3I23M1D17M
HWI-1KL149:20:C1CU7ACXX:2:2213:15510:90052/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2213:1759:92031/1 EQ|EQ|EQ    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M    K01:2123=83/56M3I41M
HWI-1KL149:20:C1CU7ACXX:2:2213:1759:92031/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:14279:12564/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:14279:12564/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16028:26845/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16028:26845/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16774:44335/1    EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2215:16774:44335/2    EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2301:16926:82641/1    EQ|EQ|EQ    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M    K01:2136=83/43M3I54M
HWI-1KL149:20:C1CU7ACXX:2:2301:16926:82641/2    EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2309:5711:82879/1 EQ|EQ|EQ    K01:2120=83/100M    K01:2120=83/100M    K01:2120=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2309:5711:82879/2 EQ|EQ|EQ    K01:1990=163/100M   K01:1990=163/100M   K01:1990=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2310:13450:61828/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2310:13450:61828/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2311:14082:99026/1    EQ|EQ|EQ    K01:2213=83/100M    K01:2213=83/100M    K01:2213=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2311:14082:99026/2    EQ|EQ|EQ    K01:2081=163/100M   K01:2081=163/100M   K01:2081=163/100M
HWI-1KL149:20:C1CU7ACXX:2:2315:4940:7934/1  EQ|EQ|EQ    K01:2133=83/100M    K01:2133=83/100M    K01:2133=83/100M
HWI-1KL149:20:C1CU7ACXX:2:2315:4940:7934/2  EQ|EQ|EQ    K01:2059=163/100M   K01:2059=163/100M   K01:2059=163/100M</h:pre>

Cited in

"Blood transcriptome analysis in a buck-ewe hybrid and its parents" Falker-Gieske, C., Knorr, C. & Tetens, J. Blood transcriptome analysis in a buck-ewe hybrid and its parents. Sci Rep 9, 17492 (2019) doi:10.1038/s41598-019-53901-z
Alejandra Bodelon, Marie Fablet, Philippe Veber, Cristina Vieira, Maria Pilar Garcia Guerreiro, High stability of the epigenome in Drosophila interspecific hybrids, Genome Biology and Evolution, 2022;, evac024, https://doi.org/10.1093/gbe/evac024
Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian fusion and centromere repositioning contributed to the formation of satellite-free centromeres during the evolution of zebras. Mol Biol Evol. 2022 Jul 26:msac162. doi: 10.1093/molbev/msac162. Epub ahead of print. PMID: 35881460.