Variant Sites Not Listed In Vcf

Question

[win]

hi all hope someone can help. The .vcf file generated after SNP calling contains variants with genotypes of 0/1 or 1/0 or 1/1.

does this mean that variants not detected in the vcf are homozygous wildtype.

is there a way to extract all such variants from the bam file an generate a file that has the QC score?

thanks in advance. ashwin

[Brad Chapman]

Ashwin -- what method are you using to call variants? Most callers have an option to enable reporting of confident reference calls as well. For instance, in GATK UnifiedGenotyper use EMIT_ALL_CONFIDENT_SITES http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html#--output_mode

Answer 1

[JC]

use samtools mpileup to call all position in your BAM -> http://samtools.sourceforge.net/samtools.shtml