VcfToBam

Last commit

vcf to bam

Usage

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

Usage: java -jar dist/jvarkit.jar vcf2bam  [options] Files

Usage: vcf2bam [options] Files
  Options:
    --bamcompression
      Compression Level. 0: no compression. 9: max compression;
      Default: 5
    --fragmentsize
      fragment size (TLEN)
      Default: 600
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    --readsize
      read size
      Default: 100
  * -r, -R, --reference
      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

  • ref
  • vcf
  • bam

See also in Biostars

Creation Date

20150612

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcf2bam/VcfToBam.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite vcf2bam ? 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

Warning

converting a bcf to a bam is like creating a cow from a steak.

VCF input must be sorted in the same order than the REF sequence.

VCF input must contain some genotypes.

Example

$ java -jar dist-1.139/vcf2bam.jar -R ref.fa  samtools.vcf.gz 2> /dev/null | grep -v "100="



@HD VN:1.5  SO:unsorted
@SQ SN:seg1 LN:5101
@SQ SN:seg2 LN:4000
@RG ID:NA12878  SM:NA12878  LB:illumina DS:NA12878
@RG ID:NA12891  SM:NA12891  LB:illumina DS:NA12891
@RG ID:NA12892  SM:NA12892  LB:illumina DS:NA12892
@CO Generated with -R /home/lindenb/src/ngsxml/test/ref/ref.fa /home/lindenb/src/ngsxml/OUT/Projects/Proj1/VCF/samtools/Proj1.samtools.vcf.gz
0000003609  83  seg1    1449    60  99=1X   =   949 -500    TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12891    NM:i:1
0000003610  147 seg1    1449    60  99=1X   =   949 -500    TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12891    NM:i:1
0000003611  147 seg1    1449    60  99=1X   =   949 -500    TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12892    NM:i:1
0000003612  83  seg1    1449    60  99=1X   =   949 -500    TGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTC    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12892    NM:i:1
0000003615  83  seg1    1450    60  98=1X1= =   950 -500    GCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12891    NM:i:1
0000003616  147 seg1    1450    60  98=1X1= =   950 -500    GCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12891    NM:i:1
0000003617  147 seg1    1450    60  98=1X1= =   950 -500    GCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12892    NM:i:1
0000003627  147 seg1    1452    60  96=1X3= =   952 -500    TTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12891    NM:i:1
0000003629  147 seg1    1452    60  96=1X3= =   952 -500    TTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12892    NM:i:1
0000003630  147 seg1    1452    60  96=1X3= =   952 -500    TTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCT    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12892    NM:i:1
0000003633  147 seg1    1453    60  95=1X4= =   953 -500    TTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCTC    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12891    NM:i:1
0000003635  83  seg1    1453    60  95=1X4= =   953 -500    TTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCTC    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12892    NM:i:1
0000003640  147 seg1    1454    60  94=1X5= =   954 -500    TAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTCTCTCA    IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII    RG:Z:NA12891    NM:i:1