how to make consensus call of diploid genotypes from bam file

[cindyz]

Hi, I'm new to the next-generation sequencing data and got confused with some concepts. Could anyone give me some help?

Take the bam files of 1000 genome data from pilot 3 as an example, I was able to use samtools to view or get consensus. But -c in pileup only give a consensus sequence. Is there a way to make consensus genotype call, including homozygous and heterozygous polymorphisms?

Thanks a lot in advance for any hint!
Cindy

[nilshomer]

Hi, I'm new to the next-generation sequencing data and got confused with some concepts. Could anyone give me some help?

Take the bam files of 1000 genome data from pilot 3 as an example, I was able to use samtools to view or get consensus. But -c in pileup only give a consensus sequence. Is there a way to make consensus genotype call, including homozygous and heterozygous polymorphisms?

Thanks a lot in advance for any hint!
Cindy

The "-c" option does give ploidy status by using IUPAC codes. Look for "K" or "R" characters (etc.) in your consensus calls.