haplotypeCaller groups comparison

Question

[David]

Hi,

I´m trying to identify variants from two groups composed of 25 samples (12 samples for the control and 12 samples for the treatment).

I´m using HaplotypeCaller as follows. My reference genome is a bacterial genome. All my samples are haploid.

gatk HaplotypeCaller --native-pair-hmm-threads $cpus --sample-ploidy 1
--reference $REF -I 1.mapped_sorted_RG.bam -I 2.mapped_sorted_RG.bam.... -I 25.mapped_sorted_RG.bam  --output variants/all.vcf

All bam files have an RG tag (see exemple below).

... MC:Z:150M MD:Z:30A68A48 RG:Z:Sample1 NM:i:2 AS:i:138 XS:i:0

I´m getting this warning. Not sure if it is normal ???

18:19:47.882 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null

The final idea is to compare samples from the two groups and identify all variants that are found at least in 30% of each group.

How would you do that ?

[Ram]

That's a warning, which can be ignored. GATK will stop if there's a serious ERROR. Wait for the VCF and examine it, it should be fine.

[David]

Great Thanks.

Once you obtain the vcf file how would you compare the two groups (normal vs treated) ?

Thanks

[Ram]

I cannot solve the scientific question for you, David. You can look at shared and exclusive variants between the two groups, but beyond that, it's all up to the questions you're asking.