Hi,
I would like to create some test data to work up various approaches to exome analysis in rare human Mendelian disorders.
I would like to modify a 'normal' exome and introduce a 'pathogenic' mutation at a specific locus. There is a mention in the quick guide to VAAST where this this was done to create a test dataset using only one chromosome's worth of data for the DHODH gene with variants as found in the Miller syndrome paper.
I would like to replicate this, but don't know how to do it. It would be useful to be able to create a variant at different allele frequencies, and be able to test various combination of % variant over the major allele.
Should I be looking to modify a Sam file, convert to bam then variant call as normal, or just add an extra variant to a VCF file, which would presumably be simpler to do?
Thanks
I would like to create some test data to work up various approaches to exome analysis in rare human Mendelian disorders.
I would like to modify a 'normal' exome and introduce a 'pathogenic' mutation at a specific locus. There is a mention in the quick guide to VAAST where this this was done to create a test dataset using only one chromosome's worth of data for the DHODH gene with variants as found in the Miller syndrome paper.
I would like to replicate this, but don't know how to do it. It would be useful to be able to create a variant at different allele frequencies, and be able to test various combination of % variant over the major allele.
Should I be looking to modify a Sam file, convert to bam then variant call as normal, or just add an extra variant to a VCF file, which would presumably be simpler to do?
Thanks