SNP scoring from a list of known SNPs

[gwilymh]

Hi,

I have recently generated a list of known SNPs from two closely related species, and am now looking to score each SNPs within each individual from my study (i.e. generate a SNP haplotype for each individual). Can anyone recommend a protocol/program for scoring a list of known SNPs for an individual. Keep in mind that some sites will be homozygous for for some individuals, even if they are polymorphic overall.

My data is presently in the form of BAM files, but can readily be converted to SAM files, mpileup files, etc.

[DZhang]

gwilymh,

GATK, samtools, and SOAPsnp are among my favorite tools for SNP analysis.

Best regards,
Douglas

https://www.contigexpress.com

[gwilymh]

Thank you DZhang.

I don't think GATK can do what I require. Do you know if it is possible with Samtools or SOAPsnp?

[DZhang]

check this review: http://www.ncbi.nlm.nih.gov/pubmed?t...%20albrechtsen
Hopefully it is helpful to you.

Best regards,
Douglas

https://www.contigexpress.com