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The tangential growth of the human visual cortex and maternal smoking during pregnancy.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches · all tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Materials and methods › Genotyping of rare variants ↔ bin/dataset_specific/extraction_snps_indels_SPARK_iWESv3.sh, the whole file · a weak match · score 0.83 · allele depth, genotype quality, gVCF, missing genotypes, Homozygous, DP
  2. [2] § Materials and methods › Genotyping of rare variants ↔ bin/dataset_specific/extraction_snps_indels_default.sh, the whole file · a weak match · score 0.82 · allele depth, genotype quality, gVCF, missing genotypes, Homozygous, DP

Paper

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The authors' code

Shell · 87 lines · 3.5 KB · Apache-2.0 · 1 match

  1. # Florian Bénitière - 21/03/2025
  2. # This script processes unique SPARK gVCF files to filter SNPs, INDELs, and non-homozygous ref sites.
  3. # It then retains only short variants (SNVs and Indels) that intersect between GATK and DeepVariant, preserving DeepVariant metadata in the output.
  5. #!/bin/bash
  7. # Exit immediately if a command exits with a non-zero status, if an undefined variable is used, or if a command in a pipeline fails
  8. set -euo pipefail
  11. # Define input arguments
  12. sample=$1 # Sample name
  13. input_gatk=$2 # Path to the GATK input file
  14. input_deepvariant=$3 # Path to the DeepVariant input file
  15. output=$4
  16. fasta_ref=$5
  17. cpu=${6:-$(nproc)} # Use provided CPU count or default to the number of available processors
  19. echo "Processing sample: ${sample}"
  20. echo "Threads used: ${cpu}"
  22. # Check if required input files exist before proceeding
  23. for file in "$input_gatk" "$input_deepvariant" "$fasta_ref"; do
  24. if [ ! -f "$file" ]; then
  25. echo "Error: File $file not found." >&2
  26. exit 1
  27. fi
  28. done
  30. # Check if required tools are installed (bcftools, tabix, bgzip)
  31. for cmd in bcftools tabix bgzip; do
  32. if ! command -v $cmd &> /dev/null; then
  33. echo "Error: $cmd is not installed." >&2
  34. exit 1
  35. fi
  36. done
  38. # Create a random temporary directory that is automatically cleaned up on exit
  39. tempdir_path=$(mktemp -d -t extraction_snps_indels_${sample}_XXXXXX)
  40. trap "rm -rf ${tempdir_path}" EXIT # Ensure cleanup on exit
  43. # Create a directory for storing intermediate and final files
  44. extension_path=${tempdir_path}${sample}
  46. # Extract and normalize SNPs/Indels from GATK, filter out homozygous ref and missing genotypes or missing metrics (DP=depth, AD=allele depth, GQ=genotype quality), and compress output
  47. bcftools view -v snps,indels --threads ${cpu} ${input_gatk} | \
  48. bcftools norm -m- --threads ${cpu} | \
  49. bcftools view -v snps,indels -e 'GT="0/0" || GT="0|0" || GT="./." || GT=".|." || FMT/DP="." || FMT/AD="." || FMT/GQ="."' --threads ${cpu} | \
  50. bcftools norm -f ${fasta_ref} --threads ${cpu} | \
  51. bcftools view -Oz -o ${extension_path}_gatk.vcf.gz
  54. # Index the compressed VCF file
  55. tabix -f ${extension_path}_gatk.vcf.gz
  58. # Extract and normalize SNPs/Indels from DeepVariant, filter out homozygous ref and missing genotypes or missing metrics (DP=depth, AD=allele depth, GQ=genotype quality), and compress output
  59. bcftools view -v snps,indels --threads ${cpu} ${input_deepvariant} | \
  60. bcftools norm -m- --threads ${cpu} | \
  61. bcftools view -v snps,indels -e 'GT="0/0" || GT="0|0" || GT="./." || GT=".|." || FMT/DP="." || FMT/AD="." || FMT/GQ="."' --threads ${cpu} | \
  62. bcftools norm -f ${fasta_ref} --threads ${cpu} | \
  63. bcftools view -Oz -o ${extension_path}_deepvariant.vcf.gz
  65. # Index the compressed VCF file
  66. tabix -f ${extension_path}_deepvariant.vcf.gz
  69. # Identify positions that are present in both DeepVariant and GATK results
  70. bcftools isec ${extension_path}_deepvariant.vcf.gz \
  71. ${extension_path}_gatk.vcf.gz \
  72. --threads ${cpu} -n=2 -w 1 -Oz -o ${extension_path}_shared_pos.vcf.gz
  75. # Extract variant information from the unique position VCF file and save as a tab-separated file
  76. (echo -e "CHROM\tPOS\tREF\tALT\tGT\tDP\tAD\tGQ"; \
  77. bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t[%GT\t%DP\t%AD\t%GQ]\n' ${extension_path}_shared_pos.vcf.gz) > \
  78. ${output%.gz}
  80. # Compress the TSV file
  81. bgzip -f ${output%.gz}
  83. # Print the number of lines in the compressed TSV file
  84. echo $(zcat ${output} | wc -l)
  86. # Print the count of unique genotype occurrences
  87. echo $(zcat ${output} | cut -f 5 | sort | uniq -c)

extraction_snps_indels_SPARK_iWESv3.sh at commit 6030cc9, under Apache-2.0 · at the source

Overview

Authors: Xavier Navarri1,2,3, Zhijie Liao1,4, James B Hengenius1, Florian Bénitière1, Sébastien Jacquemont1,5, Zdenka Pausova1,3,5, Tomáš Paus1,2,3,4
ORCID iDs: Xavier Navarri, Sébastien Jacquemont, Tomáš Paus
  1. CHU Sainte-Justine Research Centre, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada
  2. Department of Neuroscience, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, Quebec H3T 1J4, Canada
  3. Barcelonaβeta Brain Research Center, Pasqual Maragall Foundation, Carrer de Wellington, 30, Sant Martí, 08005 Barcelona, Spain
  4. Department of Psychiatry and Addictology, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, Quebec H3T 1J4, Canada
  5. Department of Pediatrics, Université de Montréal, 2900 Edouard Montpetit Blvd, Montreal, Quebec H3T 1J4, Canada
Institutions: Centre Hospitalier Universitaire Sainte-Justine (Canada); Pasqual Maragall Foundation (Spain); Barcelonaβeta Brain Research Center (Spain); CHU Sainte-Justine Research Center (Canada); Université de Montréal (Canada)
Journal: Cerebral cortex (New York, N.Y. : 1991), volume 36, issue 7, article bhag105
Dates: received 28 April 2026; accepted 19 June 2026; published online 10 August 2026; in print July 2026
Type: Research article · Language: English
License: CC BY-NC
Identifiers: DOI 10.1093/cercor/bhag105 · PMID 42574748 · PMCID PMC13456333 · OpenAlex W7202124813
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), other condition (population)
Methods: Statistics, Smoothing, state filtering, decompositions
Keywords: nicotine, prenatal exposure to maternal cigarette smoking, primary visual cortex, retinal waves
MeSH: Cigarette Smoking*, Prenatal Exposure Delayed Effects*, Visual Cortex*, Adolescent, Adult, Female, Humans, Male, Neurodevelopment, Pregnancy, Smoking, Young Adult (* major topic)
Topic: Nicotinic Acetylcholine Receptors Study (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Sainte-Justine Foundation; Université de Montréal School of Graduate Studies; Canadian Institutes of Health Research (54015, MOP-86678, MOP-74623, MOP-79571)
Citations: not cited yet (Europe PMC); 60 references in the paper

Abstract

Exposure to maternal cigarette smoking in utero is a prenatal adversity due, in part, to the pharmacological effects of nicotine. During gestation, thalamocortical inputs—generated by cholinergic retinal waves—contribute to the development of the visual cortex (V1). First, we investigated the relationship between prenatal exposure to maternal cigarette smoking (PEMCS) and the tangential growth of V1. We observed a robust association between PEMCS and V1 surface area in the UK Biobank (n = 26,987 adults, 30% exposed) and replicated this relationship in the Saguenay Youth Study (n = 944 adolescents, 47% exposed). Subsequent in silico analyses suggested that PEMCS may influence V1 prenatal growth by disrupting the proliferation of intermediate progenitor cells and inhibitory neurons. Second, we explored the role of cholinergic retinal waves as a mechanistic pathway underlying this exposure–outcome relationship. To do so, we used causal variants in genes sensitive to retinal waves (identified in retinal ganglion cells). These variants were related to V1 surface area only among exposed individuals; deletions in these genes and putative loss-of-function single-nucleotide variants were associated with lower V1 surface area. These results suggest that PEMCS influences the prenatal tangential growth of the human V1 via the retina.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

Zenodo 16268986

License: Apache-2.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Size: 1 file
Software Heritage: not checked
Found in: the text, “Genotyping of rare variants”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: pandas (8 files), BCFtools (3 files), Matplotlib (2 files), SAMtools (2 files), Snakemake (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
  • 27 September 2026: the link answers (HTTP 200)
24 files
At the source: doi.org/10.5281/zenodo.16268986

jacquemontlab/shortvariants-annotation

License: Apache-2.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 6030cc900fd5db77ceee815ec37af902806e0371, 29 June 2026
Languages: Shell (14), Python (8)
Size: 60 files, 22 scripts
Software Heritage: not archived
Found in: the Zenodo archive record
Holds: README, license file, continuous integration
Not found: CITATION.cff, environment file, tests, documentation
Tools: pandas (8 files), BCFtools (3 files), Matplotlib (2 files), SAMtools (1 file), Snakemake (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
24 files
At the source: github.com/JacquemontLab/ShortVariants-Annotation/tree/v4.0

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 44 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Data availability

UKB data is available upon request (https://www.ukbiobank.ac.uk/enable-your-research/apply-for-access). SYS data is available upon request addressed to Dr Zdenka Pausova and Dr Tomáš Paus.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 4 keywords, 12 MeSH terms, 3 funders, 60 references.

Cite

This paper

Navarri, X., Liao, Z., Hengenius, J. B., Bénitière, F., Jacquemont, S., Pausova, Z., & Paus, T. (2026). The tangential growth of the human visual cortex and maternal smoking during pregnancy. Cerebral cortex (New York, N.Y. : 1991), 36(7), bhag105. https://doi.org/10.1093/cercor/bhag105

BibTeX

@article{navarri2026tangential,
author = {Navarri, Xavier and Liao, Zhijie and Hengenius, James B and Bénitière, Florian and Jacquemont, Sébastien and Pausova, Zdenka and Paus, Tomáš},
title = {{The tangential growth of the human visual cortex and maternal smoking during pregnancy}},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
year = {2026},
month = jul,
volume = {36},
number = {7},
pages = {bhag105},
publisher = {Oxford University Press},
issn = {1047-3211},
doi = {10.1093/cercor/bhag105},
url = {https://doi.org/10.1093/cercor/bhag105},
pmid = {42574748},
pmcid = {PMC13456333}
}

RIS

TY - JOUR
AU - Navarri, Xavier
AU - Liao, Zhijie
AU - Hengenius, James B
AU - Bénitière, Florian
AU - Jacquemont, Sébastien
AU - Pausova, Zdenka
AU - Paus, Tomáš
TI - The tangential growth of the human visual cortex and maternal smoking during pregnancy
T2 - Cerebral cortex (New York, N.Y. : 1991)
J2 - Cereb Cortex
PY - 2026
DA - 2026/07/01
VL - 36
IS - 7
SP - bhag105
SN - 1047-3211
PB - Oxford University Press
DO - 10.1093/cercor/bhag105
UR - https://doi.org/10.1093/cercor/bhag105
LA - en
ER -

CSL-JSON

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