Bwa Aln For Snp/Indel Discovery With Paired End 100Bp Human Dna Reads

Question

[Travis]

Hi,

Can anyone show me a recommended command line input to achieve this? I have never used the program before and am afraid of entering inappropriate values for one of the many paramters.

Or is there a good reference dealing with the run settings for this application?

Thanks in advance,

[lh3]

The default, or if the quality is poor at tail: "aln -q15".

Answer 1

[lh3]

The default, or if the quality is poor at tail: "aln -q15". The same rule is applied to 30-120bp Illumina reads.

Answer 2

[Travis]

Does BWA require separate a separate files for each set of paired ends?

[Sean Davis]

Aligners will generally use two files for paired ends and the order is considered important.

[Travis]

What exactly do you mean by 'the order is considered important'? :)

[Travis]

Thanks Sean :) What exactly do you mean by 'the order is considered important'?

Answer 3

[Swbarnes2]

The default is probably fine.

And yes, for paired reads, you will run the aligner twice, once with the read 1 fastq, and once with read 2 fastq. You use the sampe command to make a .sam file that takes as input both alignment files. It will assume that the first read from one alignment file matches the first read in the other file, and so on, so it will set the flags and the insert size appropriately in the .sam output.

So don't quality-filter individual reads out of the fastq's, because they need to stay in paired order between the two files.

[Biomed]

What is the reason the aligners want the data in read1.fastq and read2.fastq format as in two files? Is there a theoretical or practical reason for this?