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Commit 157dcb8d authored by Brandi Cantarel's avatar Brandi Cantarel
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added bcftools stat

parent c347766c
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......@@ -250,10 +250,14 @@ process annot {
tabix ${fname}.clinvar.vcf.gz
bcftools annotate -Oz -a ${index_path}/cosmic.vcf.gz -o ${fname}.bcfannot.vcf.gz --columns CHROM,POS,ID,CNT ${fname}.clinvar.vcf.gz
java -Xmx10g -jar \$SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c \$SNPEFF_HOME/snpEff.config ${snpeff_vers} ${fname}.bcfannot.vcf.gz | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | java -Xmx10g -jar \$SNPEFF_HOME/SnpSift.jar gwasCat -db ${index_path}/gwas_catalog.tsv - |bgzip > ${fname}.annot.vcf.gz
bcftools stats ${fname}.annot.vcf.gz > ${fname}.stats.txt
plot-vcfstats -s -p ${fname}.statplot ${fname}.stats.txt
"""
else
"""
module load python/2.7.x-anaconda bedtools/2.25.0 snpeff/4.2 bcftools/intel/1.3 samtools/intel/1.3
java -Xmx10g -jar \$SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c \$SNPEFF_HOME/snpEff.config ${snpeff_vers} ${unionvcf} |bgzip > ${fname}.annot.vcf.gz
bcftools stats ${fname}.annot.vcf.gz > ${fname}.stats.txt
plot-vcfstats -s -p ${fname}.statplot ${fname}.stats.txt
"""
}
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