Cricetus cricetus bioinformatic data processing
收藏DataCite Commons2025-12-12 更新2026-01-12 收录
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https://adattar.unideb.hu/citation?persistentId=doi:10.48428/ADATTAR/T3OMKJ
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This is the bioinformatic pipeline we run to produce filtered vcf files for downstream analyses from raw reads. The steps include: (1.) demultiplexing, (2.) quality and sequence filtering, (3.) mapping to the reference, (4.) variant calling, (5.) basic filtering of vcf (imiss, meanDP, maf, biallelic, lmiss), (6.) LD pruning and keeping only SNPs. The vcf produced after step (5.) is suitable for phylogenetic tree reconstruction, the vcf produced after the last step is suitable for population genomics.
提供机构：
University of Debrecen
创建时间：
2025-12-12
