No matter how I changed the Xmx and maxReadsInMemory, I always got the same error message. Only if I changed the Xmx to 160G, it would finally work.
My question is whether it is possible for me to reduce the memory usage, and which parameter I should focus on in order to do that.
In this context no support means that we can't guarantee that the GATK tools will run successfully or accurately if you use grch38 as reference build. We have a project underway to resolve this. Some additional work is needed (not just lifting over).
Wow. 160G is a lot of memory to provide. Indel Realigner should not need that much memory.
This particular Bam file is originally from CGHUB, the barcode is TCGA-GV-A3QI-10A-01D-A21Z-08, but I realign the bam file to grch38.
The Grch38 reference that I used does have virus decoy information. I do not know if that would hurt.
Unfortunately, we do not support grch38 yet. We will soon hopefully!
Sorry, when you say "not support", do you mean gatk itself or those supportive vcf files that you used to release in a bundle?
For those vcf files, I've made some of them from the latest version of 1k genome or dbsnp and lifted them over to grch38.
Do you mean that even if I've made them, the gatk would still not function properly for grch38 input bam?
Sorry for the bother, one more question.
I downloaded old vcfs and checked those header. I noticed that each vcf has an analysis type, for instance, 1000G_phase1.indels.b37.vcf is SelectVariants, dbsnp_138.b37.vcf is LeftAlignAndTrimVariants.
Actually, that's how I prepared those vcf files. I have ALL.wgs.phase3_shapeit2_mvncall_integrated_v5a.20130502.sites.vcf, lift it over to grch38, and then use GATK -T SelectVariants to make 1000G_phase3.indels.vcf.
I am just wondering if this is the additional work that you mentioned.
@Geraldine_VdAuwera Thanks for the link! That's helpful.
I just found out that I might make a improper indel vcf file.
In v2.8 bundle, the one that works for indelrealigner is about 227M big. The one that I made is 13G, which is even bigger than 1000G_phase1.snps.high_confidence.b37.vcf (6.9G). I would assume that I've missed some cleaning steps for the preparation, which are not showing in the header.
Could you let me know how to correctly prepare those vcf files?
Hope gatk would support Grch38 sooner!