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Old 04-06-2018, 07:00 AM   #1
laurence_13
Junior Member
 
Location: Quebec

Join Date: Apr 2018
Posts: 1
Default Pooled sample for GWAS power

Hi,

I'm very new to the forum, if you have any suggestions, please share them.

So i'm working with honey bee to identify QTL associated to a resistance trait (quantitative trait) using GWAS (by calling SNPs).
Honey bee queens are diploid and males progeniture inherit 1/2 of their genes (so they are haploid).
We want to sequence the queens, but can't use them, so we sampled the males progeny. I made 4 pools of 6 males for each queen.

My question is this: Is it better to do all my pipeline to SNP calling on each of the 4 pools individually before joining the results together, or should i joint the pools raw reads before starting my pipeline to enhance statistical power?

My logic is that if I don't initially joint them, I can later compare allele frequency between each replicate to insure that rare variants are not eliminated.

thanks
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Old 04-17-2018, 04:06 PM   #2
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
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My usual approach is to do the mapping separately, and do variant calling in parallel with samtools mpileup in multi-BAM mode (i.e. using more than one BAM file on the command line). This increases the chance that a rare/odd variant will be picked up, and makes sure that all variants are called in all samples.
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