BamToMNV

MNV haplotypes

Usage

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

Usage: java -jar dist/jvarkit.jar bam2mnv  [options] Files

Usage: bam2mnv [options] Files
  Options:
    --distance
      max distance distance between two snp.
      Default: 100
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -I, --input, --bam
      add this indexed bam
      Default: []
    --mapq
      min mapping quality
      Default: 1
    --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
    -o, --out
      Output file. Optional . Default: stdout
    --pedigree, --ped
      A pedigree file. tab delimited. Columns: family,id,father,mother, 
      sex:(0|.|undefined|unknown:unknown;1|male|M:male;2|female|F:female), 
      phenotype 
      (-9|?|.:unknown;1|affected|case:affected;0|unaffected|control:unaffected) 
    -R, --reference
      For reading/writing CRAM files. Indexed fasta Reference file. This file 
      must be indexed with samtools faidx and with picard/gatk 
      CreateSequenceDictionary or samtools dict
    --tmpDir
      tmp working directory. Default: java.io.tmpDir
      Default: []
    --version
      print version and exit

Keywords

• vcf
• phased
• genotypes
• bam

Creation Date

20211208

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/phased/BamToMNV.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 bam2mnv ? 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

$ find src/test -type f -name "*.bam" > jeter.list
$ java -jar dist/bam2mnv.jar --input jeter.list src/test/resources/rotavirus_rf.vcf.gz --distance 3000

#CHROM1 POS1    REF1    ALT1    CHROM2  POS2    REF2    ALT2    distance    S1  S2  S3  S4  S5
RF03    1221    C   G   RF03    1242    C   A   22  ref v1  v1  v2  ref
RF03    1221    C   G   RF03    1688    T   G   468 ref v1  v1  ref v2
RF03    1221    C   G   RF03    1708    G   T   488 ref v1  v1  ref v2
RF03    1242    C   A   RF03    1688    T   G   447 ref ref ref v1  v2
RF03    1242    C   A   RF03    1708    G   T   467 ref ref ref v1  v2
RF03    1688    T   G   RF03    1708    G   T   21  ref ref ref ref cis
RF03    1688    T   G   RF03    2150    T   A   463 ref ref ref ref v1
RF03    1688    T   G   RF03    2201    G   C   514 ref v2  v2  .   .
RF03    1708    G   T   RF03    2150    T   A   443 .   ref ref ref v1
RF03    1708    G   T   RF03    2201    G   C   494 ref v2  v2  .   .
RF03    2150    T   A   RF03    2201    G   C   52  ref v2  v2  ref .
RF03    2150    T   A   RF03    2573    A   G   424 v1  v2  v2  ref .
RF03    2201    G   C   RF03    2573    A   G   373 .   cis cis .   .
RF04    1900    A   C   RF04    1920    A   T   21  v2  ref ref ref v1
RF05    41  T   C   RF05    499 A   T   459 ref v2  v2  v1  ref
RF05    879 C   A   RF05    1297    T   G   419 ref cis cis ref ref
RF05    1297    T   G   RF05    1339    A   C   43  ref cis cis ref .
RF06    517 C   A   RF06    543 G   C   27  .   v2  v2  .   ref
RF06    668 A   G   RF06    695 T   C   28  ref ref ref .   v1
RF07    225 C   A   RF07    684 T   G   460 ref .   .   v2  .
RF08    926 A   C   RF08    992 G   C   67  ref v2  v2  .   v1
RF09    294 T   C   RF09    317 C   A   24  .   ref ref ref v2