Hi folks
When we report variants in vcf format a common question is: what is
the coverage profile of the target region? Combining vcf and coverage
information allows to deduce also the genotypes of the target region
without variants based on the reference sequence. This is much more efficient than listing the 0/0 (which is reference genotype) at every non variant position in vcf.
For this purpose one could generate a bed file listing intervals with e.g. >10x and >20x coverage. Alternatively a wig file would be an option.
I was wondering whether there is also a possibility to include this
information in vcf. Maybe in the header? Does anyone have an idea?
thanks!
Peter
When we report variants in vcf format a common question is: what is
the coverage profile of the target region? Combining vcf and coverage
information allows to deduce also the genotypes of the target region
without variants based on the reference sequence. This is much more efficient than listing the 0/0 (which is reference genotype) at every non variant position in vcf.
For this purpose one could generate a bed file listing intervals with e.g. >10x and >20x coverage. Alternatively a wig file would be an option.
I was wondering whether there is also a possibility to include this
information in vcf. Maybe in the header? Does anyone have an idea?
thanks!
Peter
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