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JamesKane/fastq_to_sam.sh

Last active May 28, 2018 12:32
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Use GATK to create an unaligned BAM from FASTQ data
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fastq_to_sam.sh
# 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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