This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
HaplotypeCaller don't get the similar DP as IGV
I'm running HaplotypeCaller on ubuntu like this:
./gatk-126.96.36.199/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.