Commit 0cf08643 authored by peguerin's avatar peguerin
Browse files

rm INDEL

parent 0f69df6d
## remove INDEL variants from raw dDocent's output VCF file
SPECIES=$1
CONTAINER=$2
singularity exec seaconnect.simg vcftools --vcf 04-ddocent/"${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/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode --recode-INFO-all --out 05-vcf/"${SPECIES}"
\ No newline at end of file
......@@ -40,8 +40,8 @@ ln -s /entrepot/donnees/genomes/"${SPECIES}"_genome.fasta 04-ddocent/"${SPECIES}
bash 00-scripts/ddocent.sh "${SPECIES}" "${CONTAINER}" "${DDOCENT_CONFIG}"
##filter remove indels
vcftools --vcf 04-ddocent/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode-INFO-all --recode --out 05-vcf/"${SPECIES}"_snps &>10-logs/vcftools_"${SPECIES}".log
#vcftools --vcf 04-ddocent/"${SPECIES}"/TotalRawSNPs.vcf --remove-indels --recode-INFO-all --recode --out 05-vcf/"${SPECIES}"_snps &>10-logs/vcftools_"${SPECIES}".log
bash 00-scripts/rm_indels.sh "${SPECIES}" "${CONTAINER}"
#########################################################################
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