How to call SNP using known SNP information

[nkwuji]

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

[biomaseq]

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！