viola.Vcf.as_bedpe

Vcf.as_bedpe()

Convert Vcf object into Bedpe object.

Return type

Bedpe

Notes

This process is lossy because only the “positions” table and INFO tables are inherited by Bedpe class.

Examples

>>> import viola
>>> vcf = viola.read_vcf('https://raw.githubusercontent.com/dermasugita/ViolaDocs/main/docs/html/_static/tutorial.manta.vcf', patient_name='patient1')
>>> bedpe = vcf.as_bedpe()
>>> 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 Bedpe object ==> https://dermasugita.github.io/ViolaDocs/docs/html/reference/bedpe.html
        id              be1              be2 strand  qual svtype
0    test1    chr1:82550461    chr1:82554226     +-  None    DEL
1    test2    chr1:22814217    chr1:92581132     --  None    INV
2    test3    chr1:60567906    chr1:60675941     +-  None    DEL
3    test4    chr1:69583190    chr1:69590948     +-  None    DEL
4    test5  chr11:104534877  chr11:104536574     +-  None    DEL
5  test6_1  chr11:111134697   chr17:26470495     +-  None    BND
6  test6_2   chr17:26470495  chr11:111134697     -+  None    BND