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Commit 22131a46 authored by eboulanger's avatar eboulanger
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update readme

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......@@ -5,6 +5,15 @@ Scripts to prepare RADSeq data for analysis.
- outlier detection
- file conversions, subsetting and renaming
## Dependencies
You will need to install the following software:
- [VCFtools](https://vcftools.github.io)
- [BCFtools](https://samtools.github.io/bcftools/)
- [PLINK](http://zzz.bwh.harvard.edu/plink/)
You will need to have the following R packages:
## 01-SNPfiltering
script adapted from [ddocent tutorial](https://www.ddocent.com/filtering/) and additions
......@@ -41,7 +50,8 @@ bash filtering.sh ../00-rawData/02-Mullus/mullus.vcf 02-Mullus mul
| step 9 | remove sites quality score < 1/4 depth | | 17546 | | DP3g95maf05.fil5.vcf
| step 10 | depth x quality score cutoff | 424 | 15466 | |
| step 11 | He > 0.6 & Fis > 0.5 & Fix < -0.5 | 424 | 15232 | 25 min | DP3g95maf05.FIL.HFis.recode.vcf
| step 12 | rename | | | | mul_all_filtered.vcf
| step 12 | remove extreme outliers individual O HET | 413 | 15232 | 23.00 | DP3g95maf05.FIL.HFis.indHet.recode.vcf
| step 13 | rename | | | | mul_all_filtered.vcf
### SNP filtering results for Diplodus sargus
......@@ -59,8 +69,12 @@ bash filtering.sh ../00-rawData/02-Mullus/mullus.vcf 02-Mullus mul
| step 9 | remove sites quality score < 1/4 depth | 297 | 9688 | | DP3g95maf05.fil5.vcf
| step 10 | depth x quality score cutoff | 297 | 8325 | 11.00 |
| step 11 | He > 0.6 & Fis > 0.5 & Fix < -0.5 | 297 | 8206 | 27 min | DP3g95maf05.FIL.HFis.recode.vcf
| step 12 | rename | | | | dip_all_filtered.vcf
| step 12 | remove extreme outliers individual O HET | **to do** | | | DP3g95maf05.FIL.HFis.indHet.recode.vcf
| step 13 | rename | | | | dip_all_filtered.vcf
### manually rename individuals for conventional naming system
**to do**
## 02-Bayescan
......@@ -101,9 +115,8 @@ bash run_bayescan.sh
```
### step 3: verify convergence and extract outliers
Run interactive R script called `Bayescan_evaluation.R`
run 1 seems to get "best" results for diplodus. Neither runs detects outliers for mullus.
The script also extracts outlier lists and export loci positions for later subsetting
The script also extracts outlier lists for the different runs and export loci positions for later subsetting (with run index)
## 03-PCAdapt
......@@ -147,19 +160,20 @@ It also subsets the same vcf file for the remaining neutral positions and applie
filter for HWE.
Finally, the script converts the final adaptive and neutral .vcf files in .tped, .tfam,
.bed and .raw format necessary for downstream analyses.
.bed and .raw format necessary for downstream analyses.r
set arguments:
$1 = input file (vcf)
$2 = species code
$3 = bayescan run index
#### for diplodus
```
bash outlier_positions.sh ../01-SNPfilters/01-Diplodus/dip_all_filtered.vcf dip
bash outlier_positions.sh ../01-SNPfilters/01-Diplodus/dip_all_filtered.vcf dip run1
```
#### for Mullus
```
bash outlier_positions.sh ../01-SNPfilters/02-Mullus/mul_all_filtered.vcf mul
bash outlier_positions.sh ../01-SNPfilters/02-Mullus/mul_all_filtered.vcf mul run1
```
In total, 2680 adaptive loci were detected, with 10 loci detected by both the BayeScan and PCAdapt method.
After HWE filter, 12432 neutral loci were retained.
......
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