Hello!

I'm working on UMI tagged sequence data. I'm stuck in getting an desired output generated on vcf. I aligned reads using bwa mem to generate bam file. I used gatk fixmate and sorting on bam file to get an output. Later I uploaded on IGV as I can saw the mutation from T>G in IGV on desired chromosome. I've use umi-varcal tool to generate the vcf file. But I'm not getting the desired mutation that I seen on IGV in vcf file. Note-I've aligned with hg19 reference file. Can you guys give me suggestions what I've to do. Thanks!

(umi tool- https://gitlab.com/vincent-sater/umi-varcal)