Commit 32dd907f authored by peguerin's avatar peguerin
Browse files

Final.recode.vcf correction

parent 358df771
......@@ -3,4 +3,4 @@
SPECIES=$1
CONTAINER=$2
singularity exec "${CONTAINER}" vcftools --vcf 04-ddocent/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode --recode-INFO-all --out 05-vcf/"${SPECIES}"
\ No newline at end of file
singularity exec "${CONTAINER}" vcftools --vcf 04-ddocent/"${SPECIES}"/Final.recode.vcf --remove-indels --recode --recode-INFO-all --out 05-vcf/"${SPECIES}"
\ No newline at end of file
......@@ -206,7 +206,7 @@ Genotypes are stored as `VCF` files. We keep only SNPs (Single Nucleotide Polymo
SPECIES=mullus
CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
## filter VCF remove INDELs
singularity exec "${CONTAINER}" vcftools --vcf 04-ddocent/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode --recode-INFO-all --out 05-vcf/"${SPECIES}"
singularity exec "${CONTAINER}" vcftools --vcf 04-ddocent/"${SPECIES}"/Final.recode.vcf --remove-indels --recode --recode-INFO-all --out 05-vcf/"${SPECIES}"
```
Final result is generated as `VCF` files into [05-vcf](05-vcf) folder and contains only SNPs.
......
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