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Old 09-28-2011, 07:01 AM   #1
nkwuji
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Location: Dublin

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Default How to call SNP using known SNP information

Hi,

I am using samtools to call SNPs from RNA-seq data. I wonder whether I can use the known SNP frequency (or just the position of SNP) to improve my SNP calling. I know SOAPsnp can do that, but can I do that using samtools?

It seems, in samtools,

bcftools view -P 'full', 'cond2' or 'flat'

is implementing such a function. But what are the meanings of full, cond2 and flat? How can I set the prior for the known SNP?

Cheers,
Jun
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Old 07-23-2013, 09:16 PM   #2
biomaseq
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Default

Quote:
Originally Posted by nkwuji View Post
Hi,

I am using samtools to call SNPs from RNA-seq data. I wonder whether I can use the known SNP frequency (or just the position of SNP) to improve my SNP calling. I know SOAPsnp can do that
Cheers,
Jun
how did you get the konw SNP frequency?

thank you very much!
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