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Perform GWAS with gemma in a simple pipeline

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GWAS pipeline with GEMMA
=====

Simplified pipeline that requires from the user a VCF file with the samples of interest and a phenotype for each of the sample.

# Table of contents 
<div id='section-id-7'/>

- [On what platform can I work?](#section-id-7)
- [Softwares needed](#section-id-11)
- [Files needed](#section-id-24)
  - [VCF file preprocessing](#section-id-35)
    - [Subset the vcf file](#section-id-41)
    - [Remove unwanted chromosomes](#section-id-52)
    - [Keep alternative and biallelic positions only](#section-id-60)
    - [Remove indels and hide GT of individuals with low quality call](#section-id-68)
    - [Remove singletons](#section-id-83)
    - [Rename chromosomes](#section-id-117)
    - [Compress and tabix the file](#section-id-118)
    - [Get list of accessions in vcf file:](#section-id-126)
  - [Phenotype file](#section-id-139)
- [Pipeline](#section-id-154)
  - [Use a covariate](#section-id-231)
- [Analysis in R](#section-id-250)
- [User specific modifications](#section-id-274)
- [Authors](#section-id-304)
- [License](#section-id-308)
 
# On what platform can I work?
This pipeline was developed on a GNU/Linux system. It should theoretically work on Mac OS X providing that the required softwares are installed properly.

# Softwares needed
* Unix-like OS (Linux, Mac OS X, ...)
* Python 2.7 or 3.4
* R (>3.3.0) with the libraries indicated in the scripts
* Unix/Mac OS X environment for manipulation in bash
* p-link (v1.07)
* vcftools (v0.1.14)
* bcftools (v1.2)
* gemma (v0.94)

*NB: The versions indicated were the ones used and tested. One can first try already installed versions before installing the recommended version.*

# Files needed
* VCF file with the accessions/samples (can be compressed with gzip or not)
* Text file containing the order of the accessions in the VCF file (`order_accession.txt`)
* File containing the phenotypes of interest with a column containing the name of the accession
as described in the vcf file. Alternatively, one can process directly a tsv file containing
the phenotype for interest with one value per row, with the same order than for the VCF file (no header)

**Note 1: The phenotype file should be in unix format and should not contain empty lines.**

## VCF file preprocessing
Consider a VCF file containing 100 *Arabidopsis thaliana*, but the phenotype of only 80 accessions is available. The VCF file must then be first subset to these 80 accessions before being used in gemma. The VCF file input for GWAS should not contains indels, singletons, and keep only biallelic positions (non-alternative position can be removed to reduce file size). Also, the calls should be filtered by their quality for every individual, for instance a quality of minimum 25 (GQ>=25) and a coverage of minimum 3 reads (DP>=3) to keep the genotype for an individual (GT field in VCF). If the quality for a sample is not reached, the GT is turned into no data (./.).

### Subset the vcf file
list file `list_accessions_to_keep.txt` contains the ID of each accession on separate rows. Note that subsetting is possible with vcftools but takes about 8x longer. However, I use vcftools to filter genotype calls on quality and remove singletons as I did not find a simple equivalent command in bcftools (which surely exists).

```
bcftools view -S list_accessions_to_keep.txt file.vcf.gz > subset_80.vcf
```

The output file will be `subset_80.vcf`

### Remove unwanted chromosomes
Note: If you have chromosomes or organelle genomes to be excluded (mitochondria, chloroplasts, ...), you should remove them as they increase the number of SNPs to be tested and therefore decrease the threshold of significance (if Bonferroni correction is used for instance). In this case I want to keep only the 5 chromosomes of *A. thaliana*

```
bcftools view -r Chr1,Chr2,Chr3,Chr4,Chr5 subset_80.vcf > subset_80_only_chr.vcf
```

### Keep alternative and biallelic positions only
A VCF file containing multiple samples can be quite heavy although most of the lines do not contain information relevant for GWAS (no alternative allele). One can therefore remove these positions to drastically reduce the size of the file, allowing faster processing in the next steps. Keep only positions with an alternative allele (--min-ac) and only biallelic positions (--max-alleles) (1 REF + 1 ALT) with this command:

```
bcftools view --min-ac=1 --max-alleles 2  subset_80_only_chr.vcf > subset_80_only_chr_biallelic_only_alt.vcf
```

### Remove indels and hide GT of individuals with low quality call 
Two thresholds for coverage (DP) and genotype quality (GQ) are used within the [Hancock lab](https://github.com/HancockLab)

* Lenient: DP>=3 AND GQ>=25
* Stringent: DP>=5 AND GQ>=30

Depending on the stringency required, one can choose either of these thresholds.

```
vcftools --vcf subset_80_only_chr_biallelic_only_alt.vcf  \
			--minDP 3 --minGQ 25 --remove-indels --recode --recode-INFO-all \
			--out subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels
```

Note that gemma does not consider SNPs with missingness above a certain threshold (default 5%). Therefore, if in this case one SNP has less than 4 GT values (5% of 80 samples) following the filtering for DP>=3 and GQ>=25, the SNP will be ignored. Alternatively, genotypes can be imputed using BIMBAM (Plink is used in this genotype). Refer to gemma [documentation]((http://www.xzlab.org/software/GEMMAmanual.pdf)).

To remove the sites directly with VCFtools. I noticed that the function `--max-missing` was not removing all the sites with the defined percentage of missing samples. Instead, using `--max-missing-count` seems to work. In that case, 80 samples\*0.05=4 so use `--max-missing-count 4`.

```
vcftools --vcf subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels.recode.vcf \
			--max-missing-count 4 --recode --recode-INFO-all \
			--out subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing
```

### Remove singletons

Note that gemma is removing SNP under a certain allele frequency (for example 5%). Therefore, this step is optional as the singletons would be filtered in gemma.

Generates `out.singletons` (positions of all singletons)

```
vcftools --singletons --vcf subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing.recode.vcf
```

Exclude singleton positions

```
vcftools --vcf subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing.recode.vcf \
			--exclude-positions out.singletons --recode --recode-INFO-all \
			--out subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing_no_singletons
```

### Rename chromosomes

If the chromosome names contain characters, plink will replace them by 0. If no SNP information is provided in the 3rd column of the VCF file (only dots), the default SNP name (column 'rs' in gemma output) will be "chromosome:position" (e.g. Chr5:1500020). Otherwise, the chromosome information will be lost and no Manhattan plot can be plotted. To avoid this, check that the chromosome names in your VCF file are integers.

For instance, if the chromosome nomenclature is ChrX, remove the prefix "Chr" at the beginning of each line:

```
sed -i 's/^Chr//g' subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing_no_singletons.recode.vcf
```

### Compress and tabix the file

```
bgzip subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing_no_singletons.recode.vcf
tabix subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing_no_singletons.recode.vcf.gz 
```

### Get list of accessions in vcf file:

```
$ bcftool query -l subset_80_only_chr_biallelic_only_alt_DP3_GQ25_wo_indels_remove_missing_no_singletons.recode.vcf.gz > order_accession.txt
$ cat order_accession.txt
1001
1002
1003
```

## Phenotype file

Example of content for phenotype file:

```
$ cat phenotype.tsv 
12.3
13.4
15.3
```
The value 12.3, 13.4, 15.3, ... being the height of the accessions 1001, 1002, and 1003, ..., respectively.

Note: remember to convert EOLs from dos to unix format if the phenotype file is prepared in Microsoft Excel or in general on a PC. The can be easily done with the following command in a unix system: `vim phenotype.tsv -c ":set ff=unix" -c ":wq"`.

# Pipeline
Note that the GEMMA has many options which can be changed directly in [run_gwas_gemma.sh](run_gwas_gemma.sh) if needed. Refer to [GEMMA documentation](http://www.xzlab.org/software/GEMMAmanual.pdf) for more details. In this pipeline, a univariate linear mixed model performing a likelihood ratio test is used (argument `-lmm 2`). Minor allele frequency (MAF) threshold is set to 5% (default is 1%) but can be changed to for instance 10% by adding the flag `-maf 0.1` when generating the matrix and when performing the linear model fitting.

1. Generate a dataframe with all the variables and order the accessions so that they match VCF sample order
2. Generate a file for one phenotype from the previously generated dataframe (`test_export_df.txt`)
3. Process the phenotype file with plink and gemma (`run_gwas_gemma.sh`). This step should be run directly into the directory containing the vcf file and the phenotype file.
4. Import in R the output `phenotype.assoc.clean.txt` file to visualize GWAS results, see [gemma_analysis.Rmd](gemma_analysis.Rmd)

* The part 1 and 2 are done according to user pipeline to generate the genotype (R, bash, Python, ...)
* The part 3 is done in bash through the `run_gwas_gemma.sh` script. The only variables being the phenotype file given as first argument and the input vcf file as second argument (see example below) 
* The part 4 is done in R

Run the pipeline using bash:

```
bash run_gwas_gemma.sh phenotype.tsv vcf_file.vcf.gz
```

The output file is created in the subdirectory `output/`, which is automatically created by gemma from the directory containing the input vcf file. The name of the output file is `phenotype.assoc.clean.txt`. Note that the file `phenotype.assoc.txt` is the direct output of gemma but cannot be loaded by the `qqman` package in R due to a wrong organization of the column.

One log file named `phenotype.log` is generated in the same directory `output/` and contains the different parameters of the run. Example of log output:

```
LOG FILE

Command: run_gwas_gemma.sh CHH_genes_cluster6_subset_64.tsv subset_64_accessions_only_alt_wo_singletons_biallelic_only_wo_indels_minDP3_minGQ25.recode.vcf.gz
Phenotype file: CHH_genes_cluster6_subset_64.tsv
VCF file: subset_64_accessions_only_alt_wo_singletons_biallelic_only_wo_indels_minDP3_minGQ25.recode.vcf.gz
Output file: /srv/biodata/dep_coupland/grp_hancock/johan/GWAS/dna_methylation/output/CHH_genes_cluster6_subset_64.assoc.clean.txt
Run finished on Fri Nov 16 13:16:58 CET 2018
Total time of the run: 13 seconds

> Log output from GEMMA:
> ##
> ## GEMMA Version = 0.94
> ##
> ## Command Line Input = -bfile subset_64_accessions_only_alt_wo_singletons_biallelic_only_wo_indels_minDP3_minGQ25 -k /srv/biodata/dep_coupland/grp_hancock/johan/GWAS/dna_methylation/output/subset_64_accessions_only_alt_wo_singletons_biallelic_only_wo_indels_minDP3_minGQ25.cXX.txt -lmm 2 -o CHH_genes_cluster6_subset_64
> ##
> ## Summary Statistics:
> ## number of total individuals = 64
> ## number of analyzed individuals = 64
> ## number of covariates = 1
> ## number of phenotypes = 1
> ## number of total SNPs = 1566021
> ## number of analyzed SNPs = 17175
> ## REMLE log-likelihood in the null model = -114.18
> ## MLE log-likelihood in the null model = -114.937
> ## pve estimate in the null model = 0.848988
> ## se(pve) in the null model = 0.0639243
> ## vg estimate in the null model = 10.6163
> ## ve estimate in the null model = 0.73981
> ## beta estimate in the null model =   5.19004
> ## se(beta) =   0.107515
> ##
> ## Computation Time:
> ## total computation time = 0.204333 min
> ## computation time break down:
> ##      time on eigen-decomposition = 0 min
> ##      time on calculating UtX = 0.0015 min
> ##      time on optimization = 0.0626667 min
> ##

```

More details about the run is also displayed as standard output when running `run_gwas_gemma.sh` and can be redirected to a log file if needed.
```
bash run_gwas_gemma.sh phenotype.tsv vcf_file.vcf.gz > log.txt
```

## Use a covariate
A strong peak can hide other peaks. In this case, the potential causative SNP in the peak can be used as covariate and the GWAS can be run again to assess what is the weight of the other SNPs when the covariate SNP weight is removed from the analysis.
To do so one needs to generate a file with 2 columns, the first containing 1s and the second a code for the SNP to use as covariate. For example, if the SNP can be coded as 1 and the reference allele as 0, therefore, a set of 4 accessions were only the 2 first accessions have the SNP would yield a covariate file looking like this:

```
$ cat covariate_file.txt
1	1
1	1
1	0
1	0
```

This file can then be used as third argument in `run_gwas_gemma.sh` such as:

```
bash run_gwas_gemma.sh phenotype.tsv vcf_file.vcf.gz covariate_file.txt
```

### Estimate the effect of a SNP

The covariate analysis allows to assess the weight of the SNP set as covariate. To do so, compare the output in the log files with and without the covariate. One can estimate the weight of the SNP set as covariate by subtracting the PVE (phenotypic variance explained in %) values of the analysis without and with the covariate.

For instance:

Analysis without covariate

```
## Summary Statistics:
## number of total individuals = 83
## number of analyzed individuals = 83
## number of covariates = 1
## number of phenotypes = 1
## number of total SNPs = 954216
## number of analyzed SNPs = 10321
## REMLE log-likelihood in the null model = -175.057
## MLE log-likelihood in the null model = -175.918
## pve estimate in the null model = 0.942693
## se(pve) in the null model = 0.0201995
## vg estimate in the null model = 38.6983
## ve estimate in the null model = 0.906486
## beta estimate in the null model =   8.3849
## se(beta) =   0.104506

```

Analysis with covariate

```
## Summary Statistics:
## number of total individuals = 83
## number of analyzed individuals = 83
## number of covariates = 2
## number of phenotypes = 1
## number of total SNPs = 954216
## number of analyzed SNPs = 10315
## REMLE log-likelihood in the null model = -121.042
## MLE log-likelihood in the null model = -123.252
## pve estimate in the null model = 0.193322
## se(pve) in the null model = 0.165238
## vg estimate in the null model = 0.622643
## ve estimate in the null model = 1.00113
## beta estimate in the null model =   11.1001  -8.34676
## se(beta) =   0.157083  0.345247

```

The PVE explained by the SNP set as covariate is 0.942693 - 0.193322 = 0.749371 (75%). The SNP has therefore a large effect on the phenotype.

One can also estimate directly the effect of the SNP set as covariate by looking at the beta estimate given in the log file of the analysis with covariate. Here `beta estimate in the null model =   11.1001  -8.346761` indicates that the alternative allele of my SNP set as covariate reduce my phenotype by -8.34676 (in phenotype unit).

NB: When PLINK is generating the bed, bim, and fam files, it considers the reference allele of each variant as the allele with the highest frequency. This can change the interpretation of the beta in the log file from an analysis using a covariate. The beta gives an intercept and a slop value. For instance, in the example above, the value `-8.34` would have actually been `8.34` if my SNP alternative allele had a frequency > 50% in the individuals analyzed. In case of doubt, plot your phenotype by allele and you will clearly see the direction of your phenotype.

### Include several covariates

One can add several covariates in the `covariate_file.txt`, as long as the first column is made of 1s. The beta estimate will then include one intercept and a coefficient for each covariate in the same order as indicated in the `covariate_file.txt` and with the same caveat concerning the definition of the reference allele (see above).

# Analysis in R

The output file `phenotype.assoc.clean.txt` generated by gemma can be imported in R and plotted using qqman package. See the example in [gemma_analysis.Rmd](gemma_analysis.Rmd). Note that if a covariate file was used, the output file names will contain the name of the covariate file as suffix to distinguish them from the files generated with the same phenotype input but without covariate.

By default, qqman displays a blue line "suggestive line" (-log10(1e-5)) and a red line "genome-wide line" (-log10(5e-8)). They can be removed by setting `suggestiveline=FALSE, genomewideline=FALSE` in the plot command. I personally use a Bonferroni threshold instead of the 2 default thresholds displayed by the function `manhattan`. I wrote the following R function [GWAS_run.R](GWAS_run.R) which generates a QQ-plot of the p-values of each SNP and a Manhattan plot with the options to display the Bonferroni threshold and to highlight specific SNPs. Redirecting the function to a variable will store the SNPs with a significant p-value based on chosen threshold to allow further analysis.

**Examples**

Use Bonferroni threshold:

```{r}
SNP_significant <- GWAS_run(gwas.results, threshold_pvalue = "bonferroni", highlighted_SNP="4:10420088")
```

![](https://raw.githubusercontent.com/johanzi/gwas_gemma/master/images/example_manhattan_plot_GWAS_run.png)

I highlight here the SNP `4:10420088` in green. The variable `SNP_significant` is a dataframe containing the SNPs with a p-value lower than the Bonferroni threshold.

---

Use chosen threshold p-value of 5E-08:

```{r}
SNP_significant <- GWAS_run(path.file, threshold_pvalue = "5E-8", highlighted_SNP="4:10420088")
```

![](https://raw.githubusercontent.com/johanzi/gwas_gemma/master/images/example_manhattan_plot_GWAS_run_5E-08.png)

---
 
To know more about the qqman package:

* https://www.biorxiv.org/content/early/2014/05/14/005165.full.pdf+html
* https://cran.r-project.org/web/packages/qqman/qqman.pdf
* https://github.com/stephenturner/qqman

# User specific modifications

**run_gwas_gemma.sh**

-Provide the two arguments (phenotype file and VCF file). Note that the two input files should be located in the same directory.

**gemma_analysis.Rmd**

-Change dir_file and file.name variables

# Authors
* **Johan Zicola** - [johanzi](https://github.com/johanzi)

# License
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details

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