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seaconnect
annotationVariant
Commits
2968f53b
Commit
2968f53b
authored
Feb 02, 2021
by
peguerin
Browse files
check SNPs coding or not ?
parent
265698ec
Changes
1
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locate_coding_snps.sh
0 → 100644
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2968f53b
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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