jvarkit

Biostar404363

introduce artificial mutation SNV in bam

Usage

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

Usage: java -jar dist/jvarkit.jar biostar404363  [options] Files

Usage: biostar404363 [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --disable-nm
      Disable NM change. By default the value of NM is increasing to each 
      change. 
      Default: false
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --ignore-clip
      Ignore clipped section of the reads.
      Default: false
    -o, --output
      Output file. Optional . Default: stdout
  * -p, --position, --vcf
      VCF File containing the positions to change. if INFO/AF(allele 
      frequency) field is present, variant is inserted if rand()<= AF.
    -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
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit

Keywords

• sam
• bam
• variant

See also in Biostars

• https://www.biostars.org/p/404363
• https://www.biostars.org/p/416897

Creation Date

20191023

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/biostar/Biostar404363.java

Unit Tests

https://github.com/lindenb/jvarkit/tree/master/src/test/java/com/github/lindenb/jvarkit/tools/biostar/Biostar404363Test.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 biostar404363 ? 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

History

major bug detected after https://github.com/lindenb/jvarkit/issues/178 . Some reads with INDEL might have been ignored.

##Example

# look at the original bam at position 14:79838836
$ samtools tview -d T -p 14:79838836 src/test/resources/HG02260.transloc.chr9.14.bam | cut -c 1-20
     79838841  79838
NNNNNNNNNNNNNNNNNNNN
CATAGGAAAACTAAAGGCAA
cataggaaaactaaaggcaa
cataggaaaaCTAAAGGCAA
cataggaaaactaaaggcaa
CATAGGAAAACTAAAGGCAA
cataggaaaactaaaggcaa
CATAGGAAAACTAAAGGCAA
CATAGGAAAACTAAAGGCAA
CATAGGAAAACTAAAGGCAA
CATAGGAAAACTAAAGGCAA
CATAGGAAAACTAAAGGCAA
           taaaggcaa

# look at the VCF , we want to change 14:79838836 with 'A' with probability = 0.5
$ cat jeter.vcf
##fileformat=VCFv4.2
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency among genotypes, for each ALT allele, in the same order as listed">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
14	79838836	.	N	A	.	.	AF=0.5

# apply biostar404363
$  java -jar dist/biostar404363.jar -o jeter.bam -p jeter.vcf src/test/resources/HG02260.transloc.chr9.14.bam

# index the sequence
$ samtools index jeter.bam

# view the result (half of the bases were replaced because AF=0.5 in the VCF)
$ samtools tview -d T -p 14:79838836 jeter.bam | cut -c 1-20
     79838841  79838
NNNNNNNNNNNNNNNNNNNN
MATAGGAAAACTAAAGGCAA
cataggaaaactaaaggcaa
aataggaaaaCTAAAGGCAA
cataggaaaactaaaggcaa
CATAGGAAAACTAAAGGCAA
aataggaaaactaaaggcaa
AATAGGAAAACTAAAGGCAA
AATAGGAAAACTAAAGGCAA
CATAGGAAAACTAAAGGCAA
CATAGGAAAACTAAAGGCAA
AATAGGAAAACTAAAGGCAA
           taaaggcaa

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