viola.MultiVcf.as_bedpe_multi

MultiVcf.as_bedpe_multi()

Convert MultiVcf object into MultiBedpe object.

Return type

MultiBedpe

Notes

This process is lossy because only the “global_id”, “patients”, “positions” and INFO tables are inherited by MultiBedpe class.

Examples

The file tree of this script example. You can’t run this code itself, sorry!

├── this_script.py
└── vcf
    ├── patient1.vcf
    └── patient2.vcf

Here is the example code.

>>> import viola
>>> multi_vcf = viola.read_vcf_multi('./vcf', variant_caller='manta')
>>> multi_bedpe = multi_vcf.as_bedpe()
>>> multi_bedpe
INFO=imprecise,svtype,svlen,end,cipos,ciend,cigar,mateid,event,homlen,homseq,svinslen,svinsseq,left_svinsseq,right_svinsseq,contig,bnd_depth,mate_bnd_depth,somatic,somaticscore,junction_somaticscore,inv3,inv5
Documentation of MultiBedpe object ==> https://dermasugita.github.io/ViolaDocs/docs/html/reference/multi_bedpe.html
        id              be1              be2 strand  qual svtype
0    patient1_test1    chr1:82550461    chr1:82554226     +-  None    DEL
1    patient1_test2    chr1:22814217    chr1:92581132     --  None    INV
2    patient2_test1    chr1:60567906    chr1:60675941     +-  None    DEL
3    patient2_test2    chr1:69583190    chr1:69590948     +-  None    DEL
5  patient2_test3_1  chr11:111134697   chr17:26470495     +-  None    BND
6  patient2_test3_2   chr17:26470495  chr11:111134697     -+  None    BND