I am working on a haploid fungus and used GATK 4.1.7 HaplotypeCaller to call variants following the BQSR pipeline. After that, I used bcftools to merge the gvcf files followed this command:
gatk-22.214.171.124/gatk --java-options "-Xmx4g" GenotypeGVCFs -R ../../B8441.fa -V Merge.snp.gvcf -O Merge.snp.gt.gvcf
When I checked my results. I got some loci like this
1. I know .:0,0 means no calls were made at that position for that sample. Does that mean I could use the reference allele for that sample?
2. What does .:204,0:204 in position 30158 mean? It seems that the read depth for the ref (A) is 204 and for the alt (T) is 0. However when I go back to check the recal_reads.bam file for that sample, it looks like this sample has some alt (T) allele in position 30158. Could you clarify this?
Thank you very much!
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