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
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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