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Commit 2f09a2d6 authored by Brandi Cantarel's avatar Brandi Cantarel
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removing FixMate Line

parent 56d8030e
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alignment/rnaseqalign.sh
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......@@ -70,8 +70,6 @@ else
samtools view -1 --threads $SLURM_CPUS_ON_NODE -o output.bam out.sam
fi
samtools sort -@ $SLURM_CPUS_ON_NODE -O BAM -o ${pair_id}.bam output.bam
java -jar $PICARD/picard.jar FixMateInformation ASSUME_SORTED=TRUE SORT_ORDER=coordinate ADD_MATE_CIGAR=TRUE I=output.nsort.bam O=${pair_id}.bam
fi
samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.bam
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