The Genome Analysis Toolkit: A MapReduce Framework for Analyzing Next-Generation DNA Sequencing Data

• p. 5 Figure 4 legend

  given the pileup of reference bases at the current locus, and emits a call

• p. 5 Figure 4 legend

  containing the likelihoods for each of the 10 possible genotypes

• p. 5 Figure 4 code

  likelihoods[sortedList[9]] - likelihoods[sortedList[8]],

• p. 5 Figure 4 caption

  given the pileup of reference bases at the current locus

Only the authors can say what is right here.

Judge's note: Page 5 image, Figure 4 code: "ReadBackedPileup pileup = context.getBasePileup()" and "return new SimpleCall(context.getLocation(), GENOTYPE.values()[sortedList[9]].toString(), likelihoods[sortedList[9]] - likelihoods[sortedList[8]], ref.getBase())". The body text defines D as "the read base pileup at this reference base". So "pileup of reference bases" misdescribes the input, and the constructor arguments shown do not include the ten likelihoods. The SimpleCall class is not shown, so the second point is a query, not a certain error.

Second check: another model agreed

• p. 1 Abstract, lines 2–3

  Genome pilot alone includes nearly five terabases

• p. 1 Abstract

  the 1000 Genome pilot alone includes nearly five terabases

• p. 1 Abstract

  1000 Genome pilot alone

Judge's note: Page 1 image: the abstract prints "1000 Genome pilot" (singular) across a line break, while the same abstract twice prints "1000 Genomes Project". Cosmetic inconsistency in the name.

Second check: none (judge only)

• p. 2 Table 1, TraverseLoci row

  with its associated read, reference ordered data, and reference base are

Judge's note: Page 2 image confirms the Table 1 wording. The body text on the same page says the locus traversal presents "all the reads that span the genomic location", and the TraverseLocusWindows row says "the reads". The singular is a slip or shorthand; the meaning is recoverable, so this is a minor consistency point.

Second check: none (judge only)

• p. 3 Traversal types, left column

  complex assess patterns with a concomitant increase in memory

• p. 3 Traversal types, paragraph continued under Figure 1

  complex assess patterns

Judge's note: Page 3 image, left column under Figure 1, prints "complex assess patterns". The paper uses "access patterns" in the abstract, the GATK architecture section and the Discussion. Misspelling.

Second check: none (judge only)

• p. 5 Genotyper equations, sentence after p(b|G)

  {Aa,A2}

• p. 5 Genotyper equations, definition of p(b|G)

  p(b|A1) + 1

• p. 5 Simple Bayesian genotyper, text after the p(b|G) equation

  {Aa,A2} is decomposed into its two alleles

• p. 5 p(b|G) definition

  G = {Aa,A2}

Judge's note: Page 5 image: the equation uses A1 and A2, and the next line prints {A_a, A_2} with an italic subscript "a". The typo is in the PDF itself, not the text layer.

Second check: none (judge only)

• p. 5 Results, right column

  NA12878s chromosome 1 drops nearly exponentially

• p. 6 Figure 5 legend

  sample NA12878s

• p. 5 parallelization paragraph

  NA12878s chromosome 1

• p. 5 text

  drops nearly exponentially

Judge's note: Page 5 and page 6 images both print "NA12878s" with no apostrophe; the sample is named "NA12878" earlier on page 5. Cosmetic. The secondary point, that a roughly 1/N speed-up is described as "nearly exponential", is loose wording and a matter of style; it is not confirmed as a separate defect.

Second check: none (judge only)

• p. 6 Results, paragraph under Figure 5

  reducing the false-rate, can as easily be implemented in the GATK

• p. 6 Results continuation, paragraph before Discussion

  reducing the false-rate

Judge's note: Page 6 image, paragraph under Figure 5, prints "reducing the false-rate". The preceding sentence is about "many false-positive SNP calls", so "false-positive rate" is evidently intended. Dropped word.

Second check: none (judge only)

• p. 6 Discussion, first paragraph

  effect on analysis methods

• p. 6 Discussion, first paragraph

  who can focus their effect on analysis methods

Judge's note: Page 6 image, Discussion first paragraph, prints "focus their effect on analysis methods". Wrong word; "effort" is evidently meant.

Second check: none (judge only)

• p. 6 Discussion, right column

  as well

• p. 6 Discussion, right column, next line

  processing hundreds of lanes each week

• p. 6 Discussion, right column

  as well processing hundreds of lanes each week

Judge's note: Page 6 image, Discussion right column, prints "as well processing hundreds of lanes each week". Missing word.

Second check: none (judge only)

• p. 6 Acknowledgments

  during the development the Genome Analysis Toolkit

Judge's note: Viewed the crop of page 6. The Acknowledgments print "who have encouraged and supported us during the development the Genome Analysis Toolkit and have been such enthusiastic early adopters". The word "of" is missing in the page image, so this is not an extraction artefact.

Second check: none (judge only)

• p. 6 Acknowledgments

  (54 HG003067)

Only the authors can say what is right here.

Judge's note: Rests on outside knowledge: NIH grant identifiers start with a letter-prefixed activity code, and this grant's code would be U54. The page image prints "Analysis of Genomes grant (54 HG003067)" and, in the same sentence, "(U01 HG005208)", so the missing letter is in the PDF and not an extraction loss. The files do not give the correct prefix, so only the authors can confirm it.

Second check: none (judge only)