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Super Contributor
‎04-11-2018 04:05 PM
‎04-11-2018 04:05 PM
Large payment which card

I'm going to have to make a large tax payment. Looking ideas for which card to use. I will consider for apping for a new card as well. Its non-cat spend. I could do it on the CSR for the URs which I like. I could throw it on my amex hilton to get a free weekend night after 15k spend but then I am getting a bunch of hilton points which aren't the most useful currency. Cards that may give some sort of status for a large amount of spend may be useful as well. Any thoughts?

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‎04-11-2018 04:25 PM
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Re: Large payment which card

If "large" is under $50k a year*, and you expect similar tax bills in the future, maybe Blue Business Plus? No bonus, but no AF.

I pay a 1.87% fee federally and 2.3% for CA state. BBP (once it actually arrives in the mail...grr) will give me 2x MRs on up to $50k per year. I use miles well, and if my travel slows, I have a guaranteed minimum cash value via Schwab Platinum of 1.25 cpp (2.5% cash on BBP).

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From Genome Analysis Wiki
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Contents

The Variant Call Format (VCF) is a flexible file format specification that allows us to represent many different variant types ranging from SNPs, indels to copy number variations. However, variant representation in VCF is non-unique for variants that have explicitly expressed reference and alternate sequences. A failure to recognize this will frequently result in inaccurate analyses.

On this wiki page, we describe a variant normalization procedure that is well defined for biallelic as well as multiallelic variants. We then provide a formal proof the procedure's correctness.

The normalization of a variant representation in VCF consists of two parts: parsimony and left alignment pertaining to the nature of a variant's length and position respectively.

In the context of variant representation, parsimony means representing a variant in as few nucleotides as possible without reducing the length of any allele to 0. It is a property describing the nature of the length of a variant's alleles and is defined as follows:

Taking the example below, the Multi Nucleotide Polymorphism (MNP) is represented superfluously for the first 3 representations and parsimoniously for the 4th representation. When a variant has superfluous nucleotides on the left side, it is defined as not being left parsimonious as there is a need to left trim. The concept is symmetric for right parsimony and trimming. Parsimony applies to Indels too which we shall demonstrate in the left alignment section.

This figure shows multiple representations of a MNP. The left shows 4 possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the parsimonious representation of the MNP.

Based on the definition of parsimony, it is easy to see that:

However, the converse is not true.

Left aligning a variant means shifting the start position of that variant to the left till it is no longer possible to do so. It is a concept associated with insertion and deletion variants and describes specifically the nature of a position of a variant as opposed to its length. In order to further differentiate left alignment from simply left padding a variant, the definition is as follows:

The following figure shows examples of an unnormalized short tandem repeat which is a special class of indels. The color of the text is synchronized to the variant that is described in the figure.

This figure shows multiple representations of a CA tandem repeat. The left shows five possible representations differentiated by color. The right shows the corresponding representation in VCF. The last representation represents the left aligned and parsimonious representation of the STR.

In order to detect if a variant is normalized, we first prove the following lemma (1).

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