Consensus genotypes of SOAPsnp make no sense

[skblazer]

Hello,

Is there anyone familiar with soapsnp? I tried soapsnp recently for SNP calling, but cannot get any SNP calls. All of the candidate variants were not called. I cannot understand why below sites, for example, were reported as REF genotypes, considering the depth and quality are both good. I also tried feeding with different -r and -e, but similar result was generated.


chr1 204115 A A 0 T 34 2 2 A 34 2 2 4 1.00000 1.00000 0
chr1 204253 A A 0 G 38 17 17 A 0 0 0 17 1.00000 1.00000 0
chr1 206781 A A 0 T 38 18 18 A 0 0 0 18 1.00000 1.00000 0
chr1 207116 G G 0 A 35 8 8 G 0 0 0 8 1.00000 1.00000 0
chr1 207206 G G 0 C 36 17 17 G 0 0 0 17 1.00000 1.00000 0
chr1 207274 G G 0 T 37 14 14 G 0 0 0 14 1.00000 1.00000 0

Best,