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-184.108.40.206/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!
Please sign in to leave a comment.