How to automate the generation of a VCF file for

Question

[omidrouhi]

Is it possible to automate the generation of a vcf for:

chr7    140453136       .       AC      TT      100.00  PASS

instead of:

chr7    140453136       .       A       T       100.00  PASS
chr7    140453137       .       C       T       100.00  PASS

Regards,

OR

[Pierre Lindenbaum]

you must give the context of your query ( used tools, organism,... ); how do you know that both mutations belong to the same variant ?

[omidrouhi]

It is the human,a formalin fixed paraffin embedded tissue. It would require the variant calling tool that generates the vcf to recognize that the AC>TT is on the same stand (i.e. cis). If the A>T and C>T are on different strands (i.e. trans), AC>TT would be a miscall. What tool can I use?

Answer 1

[harold.smith.tarheel]

FreeBayes generates this type of allele (MNP).

Answer 2

[omidrouhi]

It is the human,a formalin fixed paraffin embedded tissue. It would require the variant calling tool that generates the vcf to recognize that the AC>TT is on the same stand (i.e. cis). If the A>T and C>T are on different strands (i.e. trans), AC>TT would be a miscall. What tool can I use?