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How-to question: Poly-ploid VCFs (variant calls) for mutational signatures
Dear everybody,
I'm new to this forum so sorry up front if this may be a duplicated question I just could find a similar thread via the search option.
I'd like to ask if anybody has has a good approach/ solution with respect to determining the mutational signatures present in (ploidy-)heterogeneous VCF files or alternatively thinks that this a waste of time:
There are mutltiple VCF files which are partially di and partially poly-ploid. Now I'd like to merge all files to normalize them together and subsequently determine the SNP-based mutational signatures using e.g. NMF. Neither VCF nor BCFtools allow merging of VCF-files of different ploidy. A possible workaround would be to transform the poly-ploid VCFs into di-ploids and merge everything afterwards but that may not lead to correct results.
1) Does anybody think this workaround will lead to reasonable mutational signatures?
2) Does anybody know what the best practice way to transform poly-ploid VCF into di-ploid is?
3) Does anybody know a software that merges VCF files of different ploidities?
I'm new to this forum so sorry up front if this may be a duplicated question I just could find a similar thread via the search option.
I'd like to ask if anybody has has a good approach/ solution with respect to determining the mutational signatures present in (ploidy-)heterogeneous VCF files or alternatively thinks that this a waste of time:
There are mutltiple VCF files which are partially di and partially poly-ploid. Now I'd like to merge all files to normalize them together and subsequently determine the SNP-based mutational signatures using e.g. NMF. Neither VCF nor BCFtools allow merging of VCF-files of different ploidy. A possible workaround would be to transform the poly-ploid VCFs into di-ploids and merge everything afterwards but that may not lead to correct results.
1) Does anybody think this workaround will lead to reasonable mutational signatures?
2) Does anybody know what the best practice way to transform poly-ploid VCF into di-ploid is?
3) Does anybody know a software that merges VCF files of different ploidities?