Can you please provide
a) GATK version used: GATK.184.108.40.206
b) Exact GATK commands used: $path2gatk HaplotypeCaller --java-options "-Xmx10G" -I $path2bam$1.marked_duplicates_sorted.bam -R $path2ref -ERC BP_RESOLUTION -O $path2output$1.BP.GATK.vcf
I am using HaplotypeCaller with BP_RESOLUTION to get the information for every base pair.
I noticed that sometimes I get no coverage using BP_resolution while I do see reads using IGV browser for example.
It is even weirder when I run two samples that are the same (same genotype but different generations - I work with Arabidopsis..). For one sample, HaplotypeCaller does see reads and for the other sample nothing. You can see enclosed the IGV browser view. I don't understand why.
Thanks a lot for your help!
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