Commit 2968f53b authored by peguerin's avatar peguerin
Browse files

check SNPs coding or not ?

parent 265698ec
SINGULARITY_SIMG=snpsdata_analysis.simg
singularity shell $SINGULARITY_SIMG
## select SNPs on an exon|CDS|mRNA|gene
intersect_vcf_annotation () {
#1 output prefix
#2 vcf
#3 gff3
#4 exon|CDS|mRNA|gene
bedtools intersect -wb -a $2 -b $3 | grep $4 | rev | cut -f10- | rev | uniq > $1_$4.bed
wait;
cat <(head $2) $1_$4.bed > $1_$4.vcf
}
# diplodus sargus
for annot in `echo "exon CDS mRNA gene"`; do intersect_vcf_annotation "diplodus" "raw/dip_adaptive_413.vcf" "annotation/sar_annotation.gff3" ${annot} ; done
# mullus surmuletus
for annot in `echo "exon CDS mRNA gene"`; do intersect_vcf_annotation "mullus" "raw/mul_adaptive_291.vcf" "annotation/mullus_annotation.gff3" ${annot} ; done
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