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We adopted a stringent call rate cut-off of ≥99%, which meant eliminating a total of 93,126 SNPs (10.3% of the 906,600 SNPs).
With a stringent call rate threshold of 95%, there were 185,150 (74.06%) polymorphic sites, 4,202 (1.68%) sites with no minor homology genotype, 180 (0.07%) monomorphic sites, and 33,742 (13.50%) sites below the call rate threshold (Table 4).
Table 3), with key tumour suppressor NKX3-1 (8p21.2) deleted in 40% of samples, and RB1 (24%), PTEN (18%), and TP53 (11%) deletions also easily detected even with very stringent call ranking selection criteria applied (see Methods).
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Set up stringent call-back targets.
In all our stringent calls for "accountability," do we ever consider that maybe we as members of a society ought to hold ourselves more accountable for all of our children?
SNP output is from polySNP tool with stringent calling (https://github.com/mfiers/polysnp).
To minimize this false negative rate (FNR) we provide a list of SNPs and INDELs using a less stringent calling criterion (5X minimum sequence coverage; Additional file 5, Table S3).
The CNVs detected in these samples were found using previously described stringent calling criteria defined for two different computer algorithms, which yields reliable CNV calls that can be experimentally validated >95% of the time (Redon et al. 2006; Marshall et al. 2008; Conrad et al. 2010; Pinto et al. 2010).
We decided to take a rather conservative attitude in terms of calling the actual miRNA genes identified and used stringent criteria calling positives.
We also used a more stringent approach called InVEx that uses a permutation-based framework to pick drivers from passengers.
It is proved that a proper factor of a polynomial can be found deterministically in polynomial time, under ERH, if its roots do not satisfy some stringent condition, called super square balanced.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com