HLI HG38 DNASeq

Summary

• VCF File Characteristics
• Sample characteristics
• High Pass Regions
• Manifest of IDs

VCF File Characteristics

• N = 2357 files
• N variants (Min,Mean,Max)
  • (4,495,629; 4,738,841; 5,846,745)
• Not phased
• Not QCed

Sample characteristics

• N=2357
• Sample volume
• DNA concentration
• DNA mass
• DNA purity 260/280 ratio

Notes:

1. There is negligible protein contamination.
2. Min mass >2220 ng, Min volume > 30 uL, Min concentration >27ng/uL
3. Ilumina usually requires a minimum of 10 nM in 20 uL
4. Min nM>80 assuming insert size of 50bp + 2x 151 bp paired-end nmer

Highpass regions

• Length
• Number
• Total length

Number of regions | chr

Total number of regions 712,265

Length of highpass regions

Length | chr

Mean length | chr 

Highpass total length | chr

2,572,251,922 (84%)

HG38 Total non-N lenght = 3,074,968,030

Manifest of IDs

• Number of individuals sent
• Number of individuals sequenced
• Number of twin pairs and zygosity
• Number of trios

Analysis of IDs

Total = Singletons + 2xTwins + Parents = 2211

Omics overlap

Meeting 2

10 Aug 2016

Summary

• Summary quality statistics chr20
• Concordance Analysis

#SNP

#InDel

#Insert / #Deletion

~1.03 in Montgomery 2013 GR

Histogram indels | novelty

Ti/Tv

ratio of transition (Ti) to transversion (Tv) ~ 2.0-2.1

Concordance Rate

number of concordant sites (that is, for the sites that share the same locus as a variant in the comp track, those that have the same alternate allele) / total

Variant call set FDR

 

dbSNP

FDR=0.08

FP=14,458

TPhat=168,759

Total=183,804

#MultiIndels / #Indels

#MultiSNP / #SNP=0.01

Multiallelic variants

Ti/Tv

Multiallelic variants

SNP Novelty Rate

knownSNPsPartial- the number of loci at which at least one allele in eval was found in the known comparison file

knownSNPsComplete- the number of loci at which all alleles in eval were also found in the known comparison file

SNPNoveltyRate- the sum of knownSNPsPartial and knownSNPsComplete divided by nMultiSNPs

Multiallelic variants

Filter Chr20: vcftools

Merge VCF: GATK CombineVariants/VCFmerge

WG HLI HG38 VCF

Convert to plink: vcftools, GATK

flip +ve strand: plink

Annotate VCF: ANNOVAR

Filter highpass regions: Bedtools

gen file

matrixeqtl file

phasing: shapeit2

GenotypeConcordance: GATK

multiallelic test

Exon HG19 vcf

Coordinate change HG38:

liftOver/crossmap

convert files: qctool / gtools

plink file

phased plink file

HLI MEETING

14 SEP 2016

CHR20 Stats

1. P HWE
2. P Heterozigozity

CHR20 Stats

All chr analysis

• Analysis conducted on SNPs shared by HLI WGS and Genotyping arrays
• Comparison of statistics with and without exclusion of individuals with high heterozygosity (Het>0.4)

Exclusions

 

• 42 individuals excluded due to high (Het>0.4) heterozygosity :
  • 5 Twin Pairs (10 individuals)
  • 22 unrelated (unpaired twins)
  • 10 parents

Discordant individuals

Heterozigosity

Heterozigosity -- F

Heterozigosity O&E ~ MAF

Relatedness ~ Zygosity

Concordance

SUM(I(PI_HAT<0.9)) = 22

SUM(I(PI_HAT<0.9)) = 5

low het individual

Individual is unrelated to any sample, including its genotyped image

disconcordance analysis

Discordant individuals:         5201,        5202,        50472,        59022,        92521

Sample swaps & low concordance

 

Sample swap within twin pairs:

HLI 5202 is actually SANGER 5201

HLI 5201 is actually SANGER 5202

Sample swaps in unpaired twins:

HLI 50472 is actually SANGER 50471

HLI 59021 is actually SANGER 59022

Individuals with low relatedness with SANGER sample:

HLI 92521 is matched to SANGER 92521 but with lower relatedness.

Unpaired twins either in SANGER of HLI:

SANGER59021

HLI50471

Comparison PLINK vs VCF

Comparison PLINK vs VCF

After removal of 16 individuals with |F|>.1

Comparison PLINK vs VCF

Before filtering SNP with MAF<0.05 and HWE<1E-6

Missing vcf file

[alvesa@athena HLI_HG38]$ ls | grep 6052
60521.vcf.gz
60521.vcf.gz.tbi

Client.Subject.ID Gender Ethnicity Birth.Date FamilyID Relation Zygosity Stool.Sample HLI.genome.ID 1731 60522 F White 10/4/35 762 Twin MZ TRUE 176500025