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jodyphelan/run_sample.sh

Created June 17, 2019 12:06
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run_sample.sh
echo $1 > $1.sample_name.txt \
&& ebiDownload.pl $1.sample_name.txt | parallel wget \
&& tb-profiler profile -1 ${1}_1.fastq.gz -2 ${1}_2.fastq.gz -t 5 -p $1 \
&& bcftools mpileup -f /home/ubuntu/refgenome/MTB-h37rv_asm19595v2-eg18.fa bam/$1.bam -a DP,AD -g 10 -B -Q 0 -q 0 -I | bcftools call -mg 10 -V indels -Oz -o vcf/$1.bcftools.g.vcf.gz \
&& gatk HaplotypeCaller -I bam/$1.bam -R /home/ubuntu/refgenome/MTB-h37rv_asm19595v2-eg18.fa -O vcf/$1.gatk.vcf.gz -ERC GVCF \
&& delly call -g /home/ubuntu/refgenome/MTB-h37rv_asm19595v2-eg18.fa -o vcf/$1.delly.bcf bam/$1.bam \
&& rm ${1}_1.fastq.gz ${1}_2.fastq.gz bam/${1}.*
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