Attention: Want an end-to-end pipelining solution for GATK Best Practices?
HaplotypeCaller don't get the similar DP as IGV
I'm running HaplotypeCaller on ubuntu like this:
./gatk-22.214.171.124/gatk HaplotypeCaller -R ~/Documents/gatk/reference/hg19.fa -I R-3.sort.bam -O R-3.gatk.raw.vcf -DF NotDuplicateReadFilter
I set the -DF NotDuplicateReadFilter because the data is amplicon sequencing data. But when I check the output, I find this location "chr10:96535124" , which DP is only 54. Next I check the igv and in the same location the total count is 2188. Why the HaplotypeCaller filter so many reads? Is that some of the parameters I set wrong?
By the way, I have tried -RF AllowAllReadsReadFilter to close all the filter, but I got the same reault.