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Old 08-21-2012, 06:05 PM   #1
Location: China

Join Date: Nov 2011
Posts: 14
Default snp calling with bwa-samtools

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!
heiya is offline   Reply With Quote
Old 08-21-2012, 06:20 PM   #2
Super Moderator
Location: US

Join Date: Nov 2009
Posts: 437

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.
adaptivegenome is offline   Reply With Quote
Old 08-21-2012, 06:27 PM   #3
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Location: china

Join Date: Jun 2011
Posts: 5

i also meet the problem,can we have a chat? my QQ:872664567
wzhjlau2009 is offline   Reply With Quote
Old 08-21-2012, 09:51 PM   #4
Location: Norway

Join Date: Jan 2011
Posts: 14

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.

oyvindbusk is offline   Reply With Quote

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