Pooled sample parameters to be used for haplotype callers
I want to use haplotype caller for detecting snps, but this time I am dealing with pooled samples.
Before pooling and doing sequencing on this WGS exp, I want to ask how GATK HAPLOTYPE CALLER deal with pooled samples. My samples are haploid in their ploidy level, so if I pool 9 samples into one, then ploidy would be 9. Can GATK haplotype caller take this as ploidy level or is it too high?
To tackle this thing I already have 9 samples from my previous sequencing, each sequenced individually. I have already called snps on them. But now I am pooling them together(concatenating the fastq files) to test how will the result look like. I would like to tell you that coverage is not an issue as I am using yeast genome. All the above 9 samples which I want to test have 100X coverage(even more).
I would like you to point me as to how should I change parameters that I can detect snps when i pooled my samples.
First of all can you please explain these 2 parametrs
--standard_min_confidence_threshold_for_calling and --standard_min_confidence_threshold_for_emitting
How can I change them when I have only 1 sample which is a 9 sample pool.
Also can you explain me this parameter
--max_alternate_alleles. By default it is 6. But I think at a position you can have 4 alleles(A,C,G,T)??
In the end should I choose 1/9th the default value of --standard_min_confidence_threshold_for_calling and --standard_min_confidence_threshold_for_emitting so as to call variants now.
Let me know if I am not clear.
Hope to hear from you soon.