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Commit 994ee16a authored by Brandi Cantarel's avatar Brandi Cantarel
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update file format svcalling

parent e56380df
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variants/svcalling.sh
+ 12
− 9
View file @ 994ee16a
...@@ -93,7 +93,7 @@ then ...@@ -93,7 +93,7 @@ then
if [[ $filter == 1 ]] if [[ $filter == 1 ]]
then then
zgrep '#CHROM' ${pair_id}.delly.vcf.gz > ${pair_id}.delly.genefusion.txt zgrep '#CHROM' ${pair_id}.delly.vcf.gz > ${pair_id}.delly.genefusion.txt
zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE ANN[*].FEATUREID FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.delly.genefusion.txt zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.delly.genefusion.txt
fi fi
elif [[ $method == 'svaba' ]] elif [[ $method == 'svaba' ]]
then then
...@@ -104,16 +104,19 @@ then ...@@ -104,16 +104,19 @@ then
svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id} svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
fi fi
#Create SV FILE #Create SV FILE
vcf-concat ${pair_id}.svaba.unfiltered*sv.vcf ${pair_id}.svaba.unfiltered*indel.vcf | vcf-sort -t temp > svaba.sv.vcf bgzip -f ${pair_id}.svaba.unfiltered.sv.vcf
bgzip -f svaba.sv.vcf bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.sv -v ${pair_id}.svaba.unfiltered.sv.vcf.gz
tabix -f svaba.sv.vcf.gz java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].DP >= 20)" | bgzip > ${pair_id}.svaba.sv.vcf.gz
bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.sv -v svaba.sv.vcf.gz -s
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].DP >= 20)" | bgzip > ${pair_id}.svaba.vcf.gz java -jar $SNPEFF_HOME/SnpSift.jar filter "( SPAN >= 20)" ${pair_id}.svaba.unfiltered.indel.vcf |bgzip > ${pair_id}.svaba.indel.vcf.gz
bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.indel -v ${pair_id}.svaba.indel.vcf.gz
java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.indel.norm.vcf.gz | bgzip > ${pair_id}.svaba.vcf.gz
if [[ $filter == 1 ]] if [[ $filter == 1 ]]
then then
zgrep '#CHROM' ${pair_id}.svaba.vcf.gz > ${pair_id}.svaba.genefusion.txt zgrep '#CHROM' ${pair_id}.svaba.sv.vcf.gz > ${pair_id}.svaba.genefusion.txt
zcat ${pair_id}.svaba.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS ALT ID ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE ANN[*].FEATUREID FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.svaba.genefusion.txt zcat ${pair_id}.svaba.sv.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS ALT ID ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.svaba.genefusion.txt
fi fi
elif [[ $method == 'lumpy' ]] elif [[ $method == 'lumpy' ]]
then then
...@@ -165,7 +168,7 @@ then ...@@ -165,7 +168,7 @@ then
mv ${pair_id}.pindel.sv.pass.vcf ${pair_id}.pindel.sv.vcf mv ${pair_id}.pindel.sv.pass.vcf ${pair_id}.pindel.sv.vcf
bgzip ${pair_id}.pindel.sv.vcf bgzip ${pair_id}.pindel.sv.vcf
zgrep '#CHROM' ${pair_id}.pindel.sv.vcf.gz > ${pair_id}.pindel.genefusion.txt zgrep '#CHROM' ${pair_id}.pindel.sv.vcf.gz > ${pair_id}.pindel.genefusion.txt
zcat ${pair_id}.pindel.sv.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHROM END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE ANN[*].FEATUREID FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.pindel.genefusion.txt zcat ${pair_id}.pindel.sv.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHROM END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u >> ${pair_id}.pindel.genefusion.txt
fi fi
elif [[ $method == 'itdseek' ]] elif [[ $method == 'itdseek' ]]
then then
......
variants/uniform_vcf_gt.pl
+ 10
− 1
View file @ 994ee16a
...@@ -26,7 +26,16 @@ while (my $line = <VCF>) { ...@@ -26,7 +26,16 @@ while (my $line = <VCF>) {
foreach $a (split(/;/,$annot)) { foreach $a (split(/;/,$annot)) {
my ($key,$val) = split(/=/,$a); my ($key,$val) = split(/=/,$a);
$hash{$key} = $val; $hash{$key} = $val;
} }
if ($alt =~ m/^chr/) {
$chr2 =~ m/(chr\w+):(\d+)/;
$chr2=$1;
$p2 = $2;
$hash{CHR2} = $chr2;
$hash{'END'} = $p2;
$annot .= ";CHR2=$chr2;END=$p2";
}
my @deschead = split(/:/,$format); my @deschead = split(/:/,$format);
my $newformat = 'GT:DP:AD:AO:RO'; my $newformat = 'GT:DP:AD:AO:RO';
my @newgts = (); my @newgts = ();
......
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