snp calling with bwa-samtools

[heiya]

hi，everyone！ I do wet experiment verification for my heterozygous snp found by bwa-samtools in rice genome recently，however only three of fourteen got experiment support， the rest didn't get！ I have checked the reads coverage in the position of SNPs， all the indication are that they are SNPs！
Could someone explain that？

all the reply are appreciated!

[adaptivegenome]

1. Sequencing error
2. Mapping error
3. Validation error.

Those are 3 possibilities, I'm sure there are more. You don't provide much info so it's hard to know for sure.

[wzhjlau2009]

i also meet the problem,can we have a chat? my email:[email protected] QQ:872664567

[oyvindbusk]

Hello heiya, my experience is that using samtools with default settings will give you a high number of false positives, this could be what you are seing.

You could try running snp-calling with the GATK using the built-in recalibration options. GATK has quite a low number of false positives. Compare the results from GATK with your existing results, and see what you get.

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