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Use GATK to create an unaligned BAM from FASTQ data
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| # USAGE: sh fastq_to_sam.sh <fastq1> <fastq2> <sample_name> <read_group> <platform_unit> | |
| gatk=~/Genomics/gatk-4.0.4.0/gatk | |
| $gatk --java-options "-Xmx8G" FastqToSam \ | |
| -FASTQ=$1 \ | |
| -FASTQ2=$2 \ | |
| -OUTPUT=$3.unmapped.bam \ | |
| -READ_GROUP_NAME=$4 \ | |
| -SAMPLE_NAME=$3 \ | |
| -LIBRARY_NAME=$3 \ | |
| -PLATFORM_UNIT=$5 \ | |
| -PLATFORM=illumina |
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