Commit 667c4ebf authored by peguerin's avatar peguerin
Browse files

readme update

parent b1f4d01c
......@@ -186,6 +186,7 @@ FreeBayes is a Bayesian genetic variant detector designed to detect SNPs, INDels
```
## global variable
SPECIES=mullus
CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
DDOCENT_CONFIG=/entrepot/working/seaconnect/seaConnect--dDocent/01-infos/ddocent_config.file
## run dDocent
......@@ -198,4 +199,17 @@ This command run dDocent workflow. It generates genotypes for each `{sample}` fo
## Generate final VCF
Genotypes are stored as `VCF` files. We keep only SNPs (Single Nucleotide Polymorphism) variants.
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Genotypes are stored as `VCF` files. We keep only SNPs (Single Nucleotide Polymorphism) variants.
```
## global variable
SPECIES=mullus
CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
## filter VCF remove INDELs
singularity exec "${CONTAINER}" vcftools --vcf 04-ddocent/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode --recode-INFO-all --out 05-vcf/"${SPECIES}"
```
# SOURCE CODE
* All the commands to run the workflow are available as a bash script [main.sh](main.sh).
* You can also run the whole workflow step by step using scripts collection [00-scripts](00-scripts.)
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