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QC.groovy
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QC.groovy
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class QC {
// Run bcftools on vcf file
static def bcftools(vcf) {
"""
bcftools stats ${vcf} > ${SarekUtils.reduceVCF(vcf)}.bcf.tools.stats.out
"""
}
// Run samtools stats on bam file
static def samtoolsStats(bam) {
"""
samtools stats ${bam} > ${bam}.samtools.stats.out
"""
}
// Run vcftools on vcf file
static def vcftools(vcf) {
"""
vcftools \
--gzvcf ${vcf} \
--relatedness2 \
--out ${SarekUtils.reduceVCF(vcf)}
vcftools \
--gzvcf ${vcf} \
--TsTv-by-count \
--out ${SarekUtils.reduceVCF(vcf)}
vcftools \
--gzvcf ${vcf} \
--TsTv-by-qual \
--out ${SarekUtils.reduceVCF(vcf)}
vcftools \
--gzvcf ${vcf} \
--FILTER-summary \
--out ${SarekUtils.reduceVCF(vcf)}
"""
}
}