Commit 5894cbd6 authored by peguerin's avatar peguerin
Browse files

no assembly ddocent

parent 53d4c40a
Variables used in dDocent Run at Thu Jun 28 16:17:31 CEST 2018
Number of Processors
64
16
Maximum Memory
0
Trimming
yes
Assembly?
yes
no
Type_of_Assembly
SE
Clustering_Similarity%
0.86
Minimum within individual coverage level to include a read for assembly (K1)
4
Minimum number of individuals a read must be present in to include for assembly (K2)
3
Mapping_Reads?
yes
Mapping_Match_Value
1
Mapping_MisMatch_Value
3
4
Mapping_GapOpen_Penalty
5
6
Calling_SNPs?
yes
Email
pierre-edouard.guerin@cefe.cnrs.fr
\ No newline at end of file
pierre-edouard.guerin@cefe.cnrs.fr
......@@ -20,7 +20,7 @@ snakemake -s 00-scripts/snakeFile.process_radtags -j 8 --use-singularity --confi
bash 00-script/demort.sh "${SPECIES}"
## rename
bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.tsv
#bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.tsv
#### with blacklist
bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.tsv 98-metrics/"${SPECIES}"_samples_blacklist.txt
......@@ -29,18 +29,19 @@ bash 00-scripts/rename.sh "${SPECIES}" 01-infos/"${SPECIES}"_sample_information.
## dDocent
CONTAINER=/entrepot/working/seaconnect/seaConnect--dDocent/seaconnect.simg
DDOCENT_CONFIG=/entrepot/working/seaconnect/seaConnect--dDocent/01-infos/ddocent_config.file
CONTAINER=/media/bigvol/eboulanger/seaconnect/seaconnect.simg
DDOCENT_CONFIG=/media/bigvol/eboulanger/seaconnect/01-infos/ddocent_config.file
#### add a reference
ln -s /entrepot/donnees/genomes/"${SPECIES}"_genome.fasta 04-ddocent/"${SPECIES}"/reference.fasta
#### run the workflow "dDocent"
cd 04-ddocent/"${SPECIES}"/
singularity exec -B "/entrepot:/entrepot" $CONTAINER dDocent $DDOCENT_CONFIG
cd ../../
bash 00-scripts/ddocent.sh "${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
#########################################################################
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