samtools error when using pipeline view/sort/index

Question

[deepue]

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?

Answer 1

[dariober]

One problem is that last line should be something like:

$SAMPATH/samtools index sorted.bam

(I haven't tested the rest but looks ok)