54 lines
1.4 KiB
Bash
54 lines
1.4 KiB
Bash
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#!/bin/bash
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:<<!
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if [ $3 == "cfDNA" ];then
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java -jar $VARSCAN somatic $1 $2\
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--output-snp $4/mutation/$5.snp.vcf \
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--output-indel $4/mutation/$5.indel.vcf \
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--min-var-freq 0.005 \
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--min-freq-for-hom 0.9 \
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--output-vcf 1 \
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--min-avg-qual 20 \
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--somatic-p-value 0.99 \
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--min-reads2 1
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java -jar $VARSCAN processSomatic \
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$4/mutation/$5.snp.vcf \
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--min-tumor-freq 0.005 \
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--max-normal-freq 0.01 \
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--p-value 0.99
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java -jar $VARSCAN processSomatic \
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$4/mutation/$5.indel.vcf \
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--min-tumor-freq 0.005 \
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--max-normal-freq 0.01 \
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--p-value 0.99
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!
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#elif [ $3 == "tissue" ];then
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java -jar $VARSCAN somatic $1 $2\
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--output-snp $3/mutation/$4.snp.vcf \
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--output-indel $3/mutation/$4.indel.vcf \
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--min-var-freq 0.01 \
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--min-freq-for-hom 0.9 \
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--somatic-p-value 0.05 \
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--output-vcf 1 \
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--min-avg-qual 20 \
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--min-coverage-normal 10 \
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--min-coverage-tumor 30 --min-reads2 3
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# --strand-filter 1
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java -jar $VARSCAN processSomatic \
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$3/mutation/$4.snp.vcf \
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--min-tumor-freq 0.01 \
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--max-normal-freq 0.01 \
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--p-value 0.05
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java -jar $VARSCAN processSomatic \
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$3/mutation/$4.indel.vcf \
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--min-tumor-freq 0.01 \
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--max-normal-freq 0.01 \
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--p-value 0.05
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#fi
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