Can you please provide
a) GATK version used: GATK.18.104.22.168
b) Exact GATK commands used :
$path2gatk HaplotypeCaller \
-I $path2bam$1.bam \
-R $path2ref \
-O $path2output_$1.GATK.vcf \
-bamout $path2output$1_out.bam \
--force-active --disable-optimizations \
You can see in the picture below two bam files. At the bottom, the original bam file and at the top, a bam file generated with the command above corresponding to the local assembly haplotypeCaller generated to call the variants. As you can see, the local assembly is definitely wrong in that region.
How could I avoid this kind of scenario?
Thank you very much!
Please sign in to leave a comment.