Omitting post-alignment processing and merging batch-based imputation: an efficient workflow for NIPT data imputation and its application in maternal folate metabolism genotyping.

Abstract excerpt

Non-invasive prenatal testing (NIPT) generates vast amounts of low-depth sequencing data, offering a valuable resource for studying maternal genetic traits. However, standard NIPT genotype imputation workflows include time-consuming post-alignment processing steps from GATK, whose benefits for low-depth data remain uncertain. Additionally, merging imputation results from large, batch-processed cohorts presents a...

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