Results!#

After running those jobs, you should be done!

Overview of the Results#

The following results should be in your output direcotry. The first tab provides a truncated results tree to help with visualization but you can see the complete tree from one pool with 6 samples in the second tab (Complete Tree).

.
├── ancestry_assignments.tsv
├── Ancestry_PCAs.png
├── common_snps_across_pools.tsv
├── file_directories.txt
├── Pool1
│   ├── bams
│   │   ├── 1.bam
│   │   ├── 1.bam.bai
│   │   ├── 2.bam
│   │   ├── 2.bam.bai
│   │   ├── 3.bam
│   │   ├── 3.bam.bai
│   │   ├── 4.bam
│   │   ├── 4.bam.bai
│   │   ├── 5.bam
│   │   ├── 5.bam.bai
│   │   ├── 6.bam
│   │   ├── 6.bam.bai
│   │   └── subset_bam.done
│   ├── individual_1
│   │   ├── common_snps
│   │   │   ├── final_subset_pruned_data.bed
│   │   │   ├── final_subset_pruned_data.bim
│   │   │   ├── final_subset_pruned_data.fam
│   │   │   ├── final_subset_pruned_data.log
│   │   │   ├── final_subset_pruned_data.pgen
│   │   │   ├── final_subset_pruned_data.psam
│   │   │   ├── final_subset_pruned_data.pvar
│   │   │   ├── snps_1000g.tsv
│   │   │   ├── SNPs2keep.txt
│   │   │   ├── snps_data.tsv
│   │   │   ├── subset_1000g.log
│   │   │   ├── subset_1000g.pgen
│   │   │   ├── subset_1000g.psam
│   │   │   ├── subset_1000g.pvar
│   │   │   ├── subset_data.log
│   │   │   ├── subset_data.pgen
│   │   │   ├── subset_data.prune.out
│   │   │   ├── subset_data.psam
│   │   │   ├── subset_data.pvar
│   │   │   ├── subset_pruned_1000g.bed
│   │   │   ├── subset_pruned_1000g.bim
│   │   │   ├── subset_pruned_1000g.fam
│   │   │   ├── subset_pruned_1000g.log
│   │   │   ├── subset_pruned_1000g.pgen
│   │   │   ├── subset_pruned_1000g.popu
│   │   │   ├── subset_pruned_1000g.prune.in
│   │   │   ├── subset_pruned_1000g.prune.out
│   │   │   ├── subset_pruned_1000g.psam
│   │   │   ├── subset_pruned_1000g.pvar
│   │   │   ├── subset_pruned_data_1000g_key.txt
│   │   │   ├── subset_pruned_data.log
│   │   │   ├── subset_pruned_data_original.pvar
│   │   │   ├── subset_pruned_data.pgen
│   │   │   ├── subset_pruned_data.psam
│   │   │   ├── subset_pruned_data.pvar
│   │   │   └── subset_pruned_data_temp.pvar
│   │   ├── freebayes_hg19.vcf
│   │   ├── freebayes_hg19.vcf.unmap
│   │   ├── freebayes.log
│   │   ├── freebayes.pgen
│   │   ├── freebayes.psam
│   │   ├── freebayes.pvar
│   │   ├── freebayes.pvar_original
│   │   ├── freebayes_tmp.pvar
│   │   ├── freebayes.vcf
│   │   ├── pca_projection
│   │   │   ├── final_subset_pruned_data_pcs.log
│   │   │   ├── final_subset_pruned_data_pcs.sscore
│   │   │   ├── subset_pruned_1000g_pcs.acount
│   │   │   ├── subset_pruned_1000g_pcs.eigenval
│   │   │   ├── subset_pruned_1000g_pcs.eigenvec
│   │   │   ├── subset_pruned_1000g_pcs.eigenvec.allele
│   │   │   ├── subset_pruned_1000g_pcs.log
│   │   │   ├── subset_pruned_1000g_pcs_projected.log
│   │   │   └── subset_pruned_1000g_pcs_projected.sscore
│   │   └── pca_sex_checks_original
│   │       ├── ancestry_assignments.tsv
│   │       ├── Ancestry_PCAs.png
│   │       └── variables.tsv
│   ├── individual_2
│   │   ...
│   ├── individual_3
│   │   ...
│   ├── individual_4
│   │   ...
│   ├── individual_5
│   │   ├── common_snps
│   │   ...
│   └── individual_6
│   └── ...
└── snps_1000g_common_across_sites.tsv

Inforamtive Results#

Your output directory will have summarized results in it (ancestry_assignments.tsv and Ancestry_PCAs.png). There are files of each individual in their separate direcotires in the pca_sex_checks_original directory (for example /path/to/parent/out/dir/Pool1/individual_1/pca_sex_checks_original/Ancestry_PCAs.png). Here’s an example of each of these;

ancestry_assignments.tsv: This file contains the predicted ancestries for all the samples as well as all the principal component locations for each individual (this will be in your output directory /path/to/parent/out/dir/ancestry_assignments.tsv). The assignments are the second to last column:

FID

IID

PC1

PC2

PC3

PC4

PC5

PC6

PC7

PC8

PC9

PC10

AFR

AMR

EAS

EUR

SAS

Final_Assignment

Pool

0

1

0.162

-0.089

-0.041

-0.014

0.059

0.010

0.028

-0.015

0.011

0.019

0

0

1

0

0

EAS

RZ731_Pool8

0

2

0.115

0.089

0.037

-0.019

0.017

0.030

0.047

0.008

-0.017

-0.012

0

0

0

1

0

EUR

RZ731_Pool8

0

3

0.147

-0.101

-0.089

-0.001

0.116

0.014

0.006

0.037

0.027

-0.035

0

0

1

0

0

EAS

RZ731_Pool8

0

4

0.150

0.108

0.023

-0.062

0.029

0.024

-0.010

-0.008

-0.034

-0.013

0

0

0

1

0

EUR

RZ731_Pool8

0

5

0.132

0.069

-0.033

-0.029

0.045

0.017

0.020

-0.011

0.011

0.023

0

0.11

0

0.89

0

EUR

RZ731_Pool8

0

6

0.149

0.105

-0.022

-0.053

0.063

0.083

-0.014

-0.029

-0.020

0.008

0

0

0

1

0

EUR

RZ731_Pool8

Ancestry_PCAs.png: a separate figure generated for each individual in each pool. For example, a PCA plot for individual 1 in Pool 1: /path/to/parent/out/dir/Pool1/individual_1/pca_sex_checks_original/Ancestry_PCAs.png.

  • This figure shows the 1000G individual locations in PC space compared to the individual. For example:

    ../_images/Ancestry_PCAs.png

  • There will be an ancestry_assignments.tsv file generated for each individual in each pool and one that has all the individuals joined together in the base output directory.

    • This file has the annotations and probabilities for each pool. For example:

    FID

    IID

    PC1

    PC2

    PC3

    PC4

    PC5

    PC6

    PC7

    PC8

    PC9

    PC10

    AFR

    AMR

    EAS

    EUR

    SAS

    combined_assignment

    Final_Assignment

    0

    Poool1

    0.137

    -0.108

    -0.0250

    -0.042

    0.032

    -0.042

    0.001

    -0.021

    -0.086

    -0.019

    0

    0

    1

    0

    0

    EAS

    EAS

Additional Results with Reference-based Exectution#

If you have reference SNP genotypes (i.e. microarray or whole exome or genome sequencing-called SNPs) and decided to estimate SNP-based ancestry, you will have additional results that compare the reference and single-cell ancestry predictions. These will be located in:

  • /path/to/parent/out/dir/reference: This will contain the ancestry predictions for the reference-based ancestry predictions per individual.

  • /path/to/parent/out/dir/ref_sc_ancestry_prediction_comparison: This will provide results on reference vs single cell based ancestry predictions. These are the main comparison files with the two most informative ones highlighted and additional information below:

snp_ancestry_predictions.tsv
reference_ancestry_numbers.png
predicted_ancestry_numbers_correct.png
predicted_ancestry_numbers_correct_identified.png
statistics_heatmap.png
predicted_numbers_statistics_heatmap_combined.png
assignments_probabilities_w_ref.png

The predicted_numbers_statistics_heatmap_combined.png figure shows the number of individuals classified to each ancestry with the single cell data and colored by if they correctly or incorrectly match the reference-annotated SNP genotype data and the heatmap below shows some statistical metrics for quantifying the single cell derived ancestry predictions:

../_images/predicted_numbers_statistics_heatmap_combined.png

The assignments_probabilities_w_ref.png figure show the probability of each sample to be classified to each of the different ancestries. This includes the reference-based predictions (microarray or whole exome or genome sequencing data) compared to the single cell based predictions

../_images/assignments_probabilities_w_ref.png