
Vignesh Ravichandran
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Activity overview
Latest activity by Vignesh Ravichandran-
Vignesh Ravichandran created a post,
CollectReadCounts : Incompatible contigs Error
I am running into imcompatible contigs error. I checked the reference fasta and the dict file with the interval file. The contigs are the same, they match (they both dont have "chr" in front of the...
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Vignesh Ravichandran commented,
The final VCF generated by GenotypeGVCFs also generates ./. for the position which has a variant in the sample level GVCF.
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Vignesh Ravichandran commented,
SkyWarrior thanks for pointing that out. It was a typo and the error still persists. I went back to the previous steps and seems like this happened in the CombineGVCFs step. I created a post about ...
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Vignesh Ravichandran commented,
Following up on this request GATK Team
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Vignesh Ravichandran created a post,
CombineGVCFs outputs null genotypes for all samples
CombineGVCFs generates ./. for all samples. Individual GVCFs have 0/0 or 0/1 sites but when combined they are all ./. and doesnt generate variant information (AC, AN or AF). These GVCFs were creat...
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Vignesh Ravichandran created a post,
[GATKv4.2] GenotypeGVCF emits non_ref sites and no AC,AN,AF
I have about 100 samples for which I generated GVCFs using haplotype caller and combined the GVCFs. The GenotypeGVCFs step emits non_ref information and no variant information including AC, AN or A...