Note that this Snakemake pipeline contains paths to the reference genome and to WhatsHap that you might need to adapt to use it.
The results of the following analysis can be found at
ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_MPI_whatshap_08232018/
To produce a chromosome-length phasing of small variants for the Ashkenazim trio, we combined variant calls from Real Time Genomics [1] with phased blocks produced by 10x Genomics [2,3,4]. The single sample 10x Genomics VCF files were combined into multi-sample VCF using bcftools and all VCFs were split by chromosome (to facilitate easy parallelization with Snakemake). Then, WhatsHap (version 0.15+14.ga105b78, [5]) was used in pedigree-aware mode [6] using the following command line:
whatshap phase --ped AJ.ped --indels --reference hg19.fasta rtg.vcf 10x-merged.vcf | bgzip > output.vcf
[1] ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/Rutgers_IlluminaHiSeq300X_rtg_11052015/rtg_allCallsV2.vcf.gz
[2] ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/10XGenomics_ChromiumGenome_LongRanger2.1_09302016/NA24143_hg19/NA24143_hg19_phased_variants.vcf.gz
[3] ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/10XGenomics_ChromiumGenome_LongRanger2.1_09302016/NA24149_hg19/NA24149_hg19_phased_variants.vcf.gz
[4] ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/10XGenomics_ChromiumGenome_LongRanger2.1_09302016/NA24385_hg19/NA24385_hg19_phased_variants.vcf.gz
[5] M. Martin, M. Patterson, S. Garg, S. O. Fischer, N. Pisanti, G. W. Klau, A. Schönhuth, T. Marschall. WhatsHap: fast and accurate read-based phasing. bioRxiv, 2016. DOI: 10.1101/085050
[6] S. Garg, M. Martin, T. Marschall. Read-Based Phasing of Related Individuals. Bioinformatics (Proceedings of ISMB), 32, pp. i234-i242, 2016. DOI: 10.1093/bioinformatics/btw276