| version | Replicates | #examples |
|---|---|---|
| v0.4 | 9 HG001 | 85,323,867 |
| v0.5 | 9 HG001 2 HG005 78 HG001 WES 1 HG005 WES(1) |
115,975,740 |
| v0.6 | 10 HG001 PCR-free 2 HG005 PCR-free 4 HG001 PCR+ |
156,571,227 |
| v0.7 | 10 HG001 PCR-free 2 HG005 PCR-free 4 HG001 PCR+ |
158,571,078 |
| v0.8 | 12 HG001 PCR-free 2 HG005 PCR-free 4 HG001 PCR+ (and, more dowsample_fraction during training) |
346,505,686 |
| version | Replicates | #examples |
|---|---|---|
| v0.5 | 78 HG001 WES 1 HG005 WES |
15,714,062 |
| v0.6 | 78 HG001 WES 1 HG005 WES(2) |
15,705,449 |
| v0.7 | 78 HG001 WES 1 HG005 WES |
15,704,197 |
| v0.8 | 78 HG001 WES 1 HG005 WES(3) |
18,683,247 |
(1): In v0.5, we experimented with adding whole exome sequencing data into training data. In v0.6, we took it out because it didn't improve the WGS accuracy.
(2): The training data are from the same replicates as v0.5. The number of examples changed because of the update in haplotype_labeler.
(3): In v0.8, we used the Platinum Genomes Truthset to create more training examples outside the GIAB confident regions.
We used: 12 HG001 PCR-free, 2 HG005 PCR-free, 4 HG001 PCR+ for training.
Among these 18 BAM files, 6 of them are from public sources:
BAM file (--reads) |
PCR-free? | FASTA file (--ref) |
Truth VCF (--truth_variants) |
BED file (--confident_regions) |
|---|---|---|---|---|
| HG001-NA12878-pFDA.merged.sorted.bam(1) | Yes | GRCh38_Verily_v1.genome.fa | NISTv3.3.2/GRCh38 | NISTv3.3.2/GRCh38 |
| NA12878D_HiSeqX_R1.deduplicated.bam(2) | No | hs37d5.fa | NISTv3.3.2/GRCh37 | NISTv3.3.2/GRCh37 |
| NA12878J_HiSeqX_R1.deduplicated.bam(2) | No | hs37d5.fa | NISTv3.3.2/GRCh37 | NISTv3.3.2/GRCh37 |
| NA12878-Rep01_S1_L001_001_markdup.bam(2) | No | hs37d5.fa | NISTv3.3.2/GRCh37 | NISTv3.3.2/GRCh37 |
| N3C9-2plex1-L1-171212B-NA12878-1_S1_L001_001_markdup.bam(3) | Yes | hs37d5.fa | NISTv3.3.2/GRCh37 | NISTv3.3.2/GRCh37 |
| NexteraFlex-2plex1-L1-NA12878-1_S1_L001_001_markdup.bam(4) | No | hs37d5.fa | NISTv3.3.2/GRCh37 | NISTv3.3.2/GRCh37 |
(1): FASTQ files from Precision FDA Truth Challenge.
(2): BAM files provided by DNAnexus.
(3): FASTQ files from
BaseSpace public data: NovaSeq S1 Xp: TruSeq Nano 350 (Replicates of NA12878)/Samples/N3C9_2plex1_L1_171212B_NA12878-1/Files/N3C9-2plex1-L1-171212B-NA12878-1_S1_L001_R1_001.fastq.gz
and N3C9-2plex1-L1-171212B-NA12878-1_S1_L001_R2_001.fastq.gz
(4): FASTQ files from
BaseSpace public data: NovaSeq S1 Xp: Nextera DNA Flex (Replicates of NA12878)/Samples/NexteraFlex_2plex1_L1_NA12878-1/Files/NexteraFlex-2plex1-L1-NA12878-1_S1_L001_R1_001.fastq.gz
and NexteraFlex-2plex1-L1-NA12878-1_S1_L001_R2_001.fastq.gz
We generated our own BAM files using BWA-MEM to map the reads to the reference, and sorts the output. We also mark duplicated reads.