SOAPsnp is able to take a SNP information file for use in calling SNPs. Unfortunately, the format of this file seems to be specific to SOAPsnp. I can pull data from NCBI's dbSNP archive but this file is in a different format AND does not contain all the information that SOAPsnp takes as input. I can parse the dbSNP files (one for each chromosome) and write to the SOAPsnp format but if this can be pulled from somewhere I don't know of, that would be preferred.
Does anyone use the -s option when using SOAPsnp?
If you use it, did you have to generate your own SNP info file?
Also, it looks like some of the attributes that SOAPsnp takes can be "zeroed" out if the data is unknown - e.g.
frequency of A,
frequency of C,
frequency of T,
frequency of G
...or given a default value if unknown - e.g.
whether the SNP is validated by experiment (1 is true, 0 is false),
whether the SNP is actually an indel (1 is true, 0 is false).
This is not the method I would prefer but I guess its better than not using the -s option at all.
Thanks,
Dan
Does anyone use the -s option when using SOAPsnp?
If you use it, did you have to generate your own SNP info file?
Also, it looks like some of the attributes that SOAPsnp takes can be "zeroed" out if the data is unknown - e.g.
frequency of A,
frequency of C,
frequency of T,
frequency of G
...or given a default value if unknown - e.g.
whether the SNP is validated by experiment (1 is true, 0 is false),
whether the SNP is actually an indel (1 is true, 0 is false).
This is not the method I would prefer but I guess its better than not using the -s option at all.
Thanks,
Dan
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