BWA and GATK pipeline

Question

[xinhui.wang]

Dear all, I am working on the raw sequencing data from X10.Is there stand pipeline of assembly and alignment to do this work. I prefer to start with BWA then GATK to do the SNP calling. Thanks and with best regards, Xinhui

[Medhat]

I did not understand,

Is there stand pipeline of assembly and alignment to do this work. I prefer to start with BWA then GATK to do the SNP calling.

what is the relation between the assembly and GATK?

If you just need to call variant as you said you will follow the GATK workflow (BWA mem > mark adaptors -> mark duplication -> find interval ... etc)

If you need to assembly this is another story

[xinhui.wang]

sorry. I mean assembly pipeline and SNP calling pipeline. BWA to do assembly and GATK to do SNP calling.

[Medhat]

BWA do alignment not assembly

so If you need to assemble and then call variant:

what comes to my mind is

• FermiKit
• and DISCOVAR

they do assembly then call variant but not with GATK

[WouterDeCoster]

I think you mean mapping/alignment instead of assembly, which organism are you working on?