I have read so many post on this website but most of them are old , I used this post to build up my pipeline, however, it is very old now (What Is The Best Pipeline For Human Whole Exome Sequencing? ).
Is there anyone who could give me a better update on
Genome Analysis Toolkit I cannot find the best way to do the steps 6 to 11 of that post and also gatk changed as mentioned below
Did you check v4 best practices? What specifically is troubling you?
Probably the "Exome" part, the Broad guides I think assume you have WGS.
@manuel.belmadani WGS is different than WES. but the process should be rather similar
Yes that's why I was suggesting that using the Broad best practices might not be completely appropriate. I'd be concerned that the base/variant recalibration steps would differ for WES. It's been asked in their forum and there's some answer about specific steps but no comprehensive guide for WES afaik.
@manuel.belmadani look at this one, outdated https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_bqsr_BaseRecalibrator.php
Yeah, I find it's difficult to adjust the individual steps if you're not following an entire guide. See my answer about using the ExAC pipeline instead.
@Santosh Anand I did check that, I am basically stuck on few steps
That is an 8 year old post where the newest answer is 4+ years old. You're better off implementing GATK Best Practices. AFAIK, building a pipeline from scratch can be quite challenging for people lacking significant experience.
@RamRS so do you have any post or something that is new and I can follow ? there are many parameters which have an affect on the output so I would like to get the use of some people experiences rather than running around myself
Not really, no. Is using a cloud platform such as Seven Bridges or GATK Firecloud an option? That might be easier froma get-it-done perspective.
@RamRS no I cannot use cloud, If I could galaxy would be a good option to use, the problem is that I don't want to just click and I have read a lot but surprisingly not many documents are out there on how one can progress