Versions used: -gatk-184.108.40.206
-openjdk version 11.0.8
HaplotypeCaller --emit-ref-confidence GVCF --output denemegatkvar.gvcf --input Documents/sorted.bam --reference Documents/hg19.fa
HaplotypeCaller --output denemegatkvar.vcf --input Documents/sorted.bam --reference Documents/hg19.fa
Greetings GATK community!
I need some help in an issue I could not be sure if it's a known feature or a bug
While I was working on a project, I noticed some differences in variant lines between gvcf and vcf files, both produced by HaplotypeCaller(as indicated in code above, respectively).
These differences include quality, DP values, as well as some additional variant lines with no genotype/coverage info in gvcf file, which are completely absent in the vcf file.
When the positions are looked in IGV, it seems that -ERC GVCF have found the variants (but failed to give any genotype/coverage info, even though there seems many reads), whereas vcf call didn't find (or filtered out due to the quality score) these lines.
--vcf lines screentshot
For my project, I need to extract coverage infos, therefore these lines pose a problem. If it was a known issue, please have the patience to explain the reason why it happens and if there's a way to overcome this issue.
Thanks in advance
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