How to call SNP's from the consensus file obtained from soapsnp?

Question

[lakhujanivijay]

I have obtained the consensus file by running soapsnp; see below:

soapsnp -i file.soap.sorted -d genome.fa -o consensus.out -r 0.0001 -t -u -L 251 -M chrN.mat -m

How to call SNP's from the consensus file obtained from soapsnp?

Answer 1

[Prash]

I was wondering if everyone tried using the samtools sorted bam file for obtaining soapsnp consensus. Ideally, the format seems to be the same. Isn't it?

Thanks Prash