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Old 08-25-2011, 01:19 AM   #9
Location: Hitchin, UK

Join Date: Oct 2010
Posts: 15

Originally Posted by TuA View Post
The problem is that samtools is the only software (at least that I know of) which provides the 'raw.vcf' format, ie the information for all sequenced sites (not only SNP positions). This format is required to be able to compare data among individuals (population genomics). Working with pure SNP tables, I will not be able to distinguish if a particular polymorphic position has not been sequenced in individual A or if individual A is homozygous for the reference allele.
The GATK Unified Genotyper can do this too. Check the --output_mode option on It sounds like you want EMIT_ALL_CONFIDENT_SITES or EMIT_ALL_SITES.

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