samtools error when using pipeline view/sort/index
Hi,
I have tried to use the below pipeline based on the suggestion in this post.
$BWAPATH/bwa mem $REFPATH/hg19 $DATPATH/R1.fastq.gz $DATPATH/R2.fastq.gz | $SAMPATH/samtools view -Sb - | $SAMPATH/samtools sort - sorted && $SAMPATH/samtools index - > $DATPATH/sorted.bam
The subsequent step is failing with error message sorted.bam is not coordinate sorted.
To my surprise, though the above step has completed successfully, it created an empty file.
Could you please help me understand what might be the reason?
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