Question: haplotypeCaller groups comparison
0
gravatar for David
9 months ago by
David160
David160 wrote:

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 ?

gatk • 293 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by David160

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.

ADD REPLYlink written 9 months ago by RamRS24k

Great Thanks.

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

Thanks

ADD REPLYlink written 9 months ago by David160

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.

ADD REPLYlink written 9 months ago by RamRS24k
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