Variant Calling Workflow: example has incorrect samtool sort options and param

[msuhovec]

We taught the variant calling lesson here at Notre Dame on 3/4/20.

At one point in the lesson, this use of samtools sort is given:

Sort BAM file by coordinates
Next we sort the BAM file using the sort command from samtools. -o tells the command where to write the output.

$ samtools sort -o results/bam/SRR2584866.aligned.sorted.bam results/bam/SRR2584866.aligned.bam 

We are using samtools version 1.9 here, and with version there are several problems with the example:

1. The -o option will send the output to standard out
2. The source and destination parameters are swapped.
3. A destination file name is given, rather than a file prefix- this results in a results file ending in bam.bam

The usage syntax that worked fro us was:

samtools sort results/bam/SRR2584866.aligned.bam results/bam/SRR2584866.aligned.sorted

`

[fpsom]

Hi @msuhovec ! Thank you for your comment and for raising this issue. I remember testing the exact commands with no issues, so I am a bit perplexed as to why this happened.

Looking through the samtools manual here it says the following:

The sorted output is written to standard output by default, or to the specified file (out.bam) when -o is used. 

Additionally, swapping source and destination should not matter, given that the -o is specified.

Also, I just tried the command (locally, and not on the Amazon image) and it seems to work fine. However, it is a distinct possibility that this was an issue in the image directly.

During the workshop, did you use a local installation, or the Carpentries-provided Amazon instance?