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positions not being reported when using GENOTYPE_GIVEN_ALLELES
Here is my command:
java -jar GenomeAnalysisTK.jar -T HaplotypeCaller -R GRCh37-lite.fa --disable_read_filter DuplicateRead -I myBam.bam --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles all.gatk.sorted.vcf -o test.vcf -L all.gatk.sorted.vcf
This seems to work well, but there are a few variants in all.gatk.sorted.vcf whose positions don't show up in test.vcf.
I can look in the bam file and see that there is coverage in the positions of interest. I can also confirm that there are many positions in my list for which the bam doesn't have a variant in the reads and it gets reported correctly, so I don't think the issue is with having any of the files read correctly, or negative reporting.
I'm looking at amplicon data which have a very irregular coverage profile and I am using version 3.4-46-gbc02625
Has anyone seen this sort of problem, or can anyone suggest a solution?