Additional files for Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

Chinese Quartet Genome 

In this repository, we provided some additional files for Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet.

Additional Files 

• Additional file4_CSV.evidence.pdf:
  • Manually curated candidate CSVs of the twins in Chinese Quartet.
• Additional file5_denovo_somatic.evidence.pdf
  • Manually curated candidate de novo and somatic mutations of the twins in Chinese Quartet.
• Additional file6 potential_FP_FN.pdf
  • Manually curated potential false positives and false negative of Chinese Quartet benchmarks.

Other publihsed files

• Variants of the standard reference by Illumina reads are downloaded from https://zenodo.org/record/5275189#.YaaYn9DMJPZ. 
• Small variants for HG002 are downloaded from GIAB FTP site at https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/latest/GRCh38/HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz. 
• Large variants for HG002 are downloaded from https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz. 
• Variants for HGSVC samples are downloaded at http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/