Update vcftobedpe to support Delly 0.7.8 ouputs#311
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whelena wants to merge 4 commits intohall-lab:masterfrom
Open
Update vcftobedpe to support Delly 0.7.8 ouputs#311whelena wants to merge 4 commits intohall-lab:masterfrom
whelena wants to merge 4 commits intohall-lab:masterfrom
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I have vcf outputs from delly which do not have an ALT field for SVTYPE=BND, instead the info is recorded in the INFO field under MATECHROM, MATEPOS and MATESTRAND.
I added a few lines in the vcftobedpeconverter.py to add this option.