I am trying to compare the genotypes from sequence data (GA2) to those of an Illumina array chip.
I used MAQ to align the sequence data, which made it very easy to obtain information about read depth and consensus quality for VARIANT sites via the cns.final.snp file.
Unfortunately, if a SNP is not listed in this file (because it was either not covered, low quality, homozygous referent, etc.), I must use the cns2view command to obtain the same types of information about it. This is fine, but I would also like to pass these sites through the same set of quality filters as cns.final.snp.
Thus, I tried to run my cns.view file through SNPFilter using the same parameters that were used to produce cns.final.snp. 2 problems resulted. First, the list of remaining sites was much lower than that of cns.final.snp (108,492 cns.final.view, 186,232 cns.final.snp). This seems strange since cns.view contains all the same information as cns.snp and more! Second, I realized that neither of the cns.final.* files are being filtered on concensus quality (column 5 in cns.snp), even though the parameter (-q) is set to 40.
Can anyone provide insight to these problems?
Can SNPFilter only be used with variant sites? If so, can someone suggest a way to replicate the filters so that I can apply them to other sites.
What is up with the -q parameter? Why does it not seem to be doing anything?
Thanks in advance for any assistance!
I used MAQ to align the sequence data, which made it very easy to obtain information about read depth and consensus quality for VARIANT sites via the cns.final.snp file.
Unfortunately, if a SNP is not listed in this file (because it was either not covered, low quality, homozygous referent, etc.), I must use the cns2view command to obtain the same types of information about it. This is fine, but I would also like to pass these sites through the same set of quality filters as cns.final.snp.
Thus, I tried to run my cns.view file through SNPFilter using the same parameters that were used to produce cns.final.snp. 2 problems resulted. First, the list of remaining sites was much lower than that of cns.final.snp (108,492 cns.final.view, 186,232 cns.final.snp). This seems strange since cns.view contains all the same information as cns.snp and more! Second, I realized that neither of the cns.final.* files are being filtered on concensus quality (column 5 in cns.snp), even though the parameter (-q) is set to 40.
Can anyone provide insight to these problems?
Can SNPFilter only be used with variant sites? If so, can someone suggest a way to replicate the filters so that I can apply them to other sites.
What is up with the -q parameter? Why does it not seem to be doing anything?
Thanks in advance for any assistance!
Comment