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It is generally recommended that pooled population samples (meaning a pool of individuals from a population sequenced without barcodes) be analyzed using SNP callers that are specific to this type of data.
However, with the programs I have tried, (freebayes and GATK with the -ploidy tag) the output is, as expected, polyploid. So a SNP might have this as its call:
0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/1/1/1/1/1/1/1/1/1/1:13,5:18:0:10:0.250
Which is fine, but it is also completely incompatible with almost all downstream applications.
The alternative of course is SNP callers that shove the allele frequency into a 0/0 0/1 1/1 basket.
Are there programs I don't know about that work with this type of data? Is there a better way of doing these analyses?
However, with the programs I have tried, (freebayes and GATK with the -ploidy tag) the output is, as expected, polyploid. So a SNP might have this as its call:
0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/1/1/1/1/1/1/1/1/1/1:13,5:18:0:10:0.250
Which is fine, but it is also completely incompatible with almost all downstream applications.
The alternative of course is SNP callers that shove the allele frequency into a 0/0 0/1 1/1 basket.
Are there programs I don't know about that work with this type of data? Is there a better way of doing these analyses?
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