Single Individual Genotyping After Solid Mate-Pair Sequencing

Question

[Vova Naumov]

Hi! We have reads of a single individual from SOLiD mate-pair, mapped to hg18 (at moment, but we can go to hg19). And I'd like to genotype this individual and get genotypes at all needed positions (rs list or bed file with snps) For moment I tried lifescope (which gives only variants different from hg18), GATK Unified Genotyper and samtools, but if I understand right - that tools are for multiple genomes. Could you please give me links to some tutorials or tools that are useful for this task? Thank you

Answer 1

[Sean Davis]

Are your mapped data in BAM format? If so, then the documentation for samtools mpileup and GATK Unified Genotyper on the respective sites should be plenty. Both tools work fine with a single BAM file.