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seaconnect
annotationVariant
Commits
8a954591
Commit
8a954591
authored
Mar 05, 2021
by
peguerin
Browse files
from a table select only nonsynonymous variants
parent
17cd06f2
Changes
1
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Inline
Side-by-side
keep_synonymous.sh
0 → 100644
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8a954591
anvage synonymous
--vcf
diplodus_CDS.vcf
\
--genome
genomes/diplodus_genome_lgt6000.fasta
\
--annotation
annotation/sar_annotation.gff3
\
--output_prefix
diplodus_CDS
vcftools
--positions
<
(
awk
'{print $1" "$2}'
diplodus_CDS_uniprot_blast_filtered.tsv |
sort
|
uniq
)
--vcf
diplodus_CDS_nonsynonymous.vcf
--recode
--out
diplodus_CDS_uniprot_nonsynonymous
grep
-v
"^#"
diplodus_CDS_uniprot_nonsynonymous.recode.vcf |
awk
'{ print $1"\t"$2}'
|
while
read
CHROMPOS
;
do
grep
"
$CHROMPOS
"
diplodus_CDS_uniprot_blastx.tsv
;
done
>
diplodus_CDS_uniprot_nonsynonymous.tsv
nonsynonymous_chrompos
()
{
#1 vcf input
#2 genome fasta
#3 genome gff3
#4 prefix
#5 uniprot table
anvage synonymous
--vcf
$1
\
--genome
$2
\
--annotation
$3
\
--output_prefix
$4
vcftools
--positions
<
(
awk
'{print $1" "$2}'
$5
|
sort
|
uniq
)
--vcf
$4
"_nonsynonymous.vcf"
--recode
--out
$4
"_uniprot_nonsynonymous"
grep
-v
"^#"
$4
"_uniprot_nonsynonymous.recode.vcf"
|
awk
'{ print $1"\t"$2}'
|
while
read
CHROMPOS
;
do
grep
"
$CHROMPOS
"
$5
;
done
>
$4
"_uniprot_nonsynonymous.tsv"
}
nonsynonymous_chrompos
(
"mullus_CDS.vcf"
,
"genomes/mullus_genome_lgt6000.fasta"
,
"annotation/mullus_annotation.gff3"
,
"mullus_CDS"
,
"mullus_CDS_uniprot_blast_filtered.tsv"
)
\ No newline at end of file
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