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Commit fb9e02ce authored by Brandi Cantarel's avatar Brandi Cantarel
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itdseek with hardcoding

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variants/svcalling.sh
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...@@ -154,7 +154,7 @@ fi ...@@ -154,7 +154,7 @@ fi
if [[ $method == 'itdseek' ]] if [[ $method == 'itdseek' ]]
then then
stexe=`which samtools` stexe=`which samtools`
samtools view -@ $NPROC -L ${bed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${bed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz samtools view -@ $NPROC -L ${bed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${bed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
tabix ${pair_id}.itdseek.vcf.gz tabix ${pair_id}.itdseek.vcf.gz
bcftools norm --fasta-ref $reffa -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx30g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz bcftools norm --fasta-ref $reffa -m - -Ov ${pair_id}.itdseek.vcf.gz | java -Xmx30g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
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