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SNPs not filtered out in hard filtering
I hope you can give me some help or advice on the hard filtering of the SNPs.
I'm working on the lovebird genome and my reference genome is a young male (we did the assembly) and its parents are mapped against his genome to identify SNPs for development of a parentage verification panel.
During the step where I extract the variants I get 1 428 879 variants for the father and 1 916 289 for the mother.
When I apply the hard filtering parameters I get 150 variants less for the mother but two variants more for the father.
What worries me is that I have applied two sets of parameters for both parents and both times I have gotten the same results. These were:
QD<2 / FS > 60 / MQ < 40 / MQRankSum < -12.5 / ReadPosRandSum < -8.0
Here all the variants PASSED and none had FILTERED out
Then I applied the following:
QD > 2 / FS < 10 / MQ > 50 / MQRankSum > -5.0 / ReadPosRandSum < -8.0
Once again all the variants PASSED and there was no difference to the first set of parameters
Can you perhaps suggest anything that I can do/