I have been quite busy for sometimes now using this package. No offend but I found it bloody useless at least from being straightforward if one wants to use it.
1- how one can ask for a help ? ( just google how to ask a question, you go to a page where there is nothing allowing you to ask any question, of course I registered a week ago). there are many many issues, one says use queue one says don't use it.
one says align , the other says don't need and I read few papers in high end journals where all used different platforms !!!
2- all their ridiculous post are old , useless and not clear
3- version 3 is different from version 4, yet both you must have java 1.8 (don't use any higher)
if you use bwa or whatever, you cannot find a way to use GATK for alignment , I have been killing myself to get it to match with no success !!! if you know how, show me please
I even tried to use an older version but I cannot find a way to get it to work. Is there someone who could direct me to a good source for it? or show me how to report my errors on the GATK web?
I am even trying to use cloud now, if anyone knows how to do that I would appreciate any guide
Ok, it seems like I need to take some serious actions :-) I summaries steps I could find, now if you could please help me find each steps command so that we all go home in peace :-)
Step 1 ----> Get your data forward and revers
Step 2 ----> Map with BWA mem (dont do it with other BWA)
Step 3 ----> Sam to Bam (you can use whater you like I use BWA)
Step 4 ----> Mark Duplicate reads (I use PICARD)
Step 5 ----> Uses samtools flagstat command to print descriptive information for a BAM dataset you generated in step 3
Step 6 ----> samtools mpileup multi-way pileup of variants
Step 7 ----> VarScan for variant detection
Step 8 ----> Annotate (You can use so many algithms, which one is the best? God KNOWS, maybe
VCFannotateGenotypes I dont know)
Step 9 ----> You can filter your VCF data in a variety of attributes (is it necessary? God knows again)
Step 10 ---> ANNOVAR Annotate VCF
Step 11 ---> Go get a damn beer because you went through a lot