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The information comes from PGT tag, I can ask GATK not to output this with option "--doNotRunPhysicalPhasing"
The GATK version is 184.108.40.206 and the command is First step: gatk HaplotypeCaller -R /work7_P1/GATK_RegionCall/IRGSP-1.0/IRGSP-1.0_genome.fasta -I /work7_P1/GATK_RegionCall/Bam_SortIndex/B001.g.vcf -O /work7_P1/GATK_RegionCall/Variant_call/B001.g.vcf…
Thank you so much @AdelaideR, The downstream analysis I would like to do is to accurately construct the alternate reference genome for some specific regions. To be able to do that, I need to identify all reliable differences between the reference …
@bhanuGandham Thank you
@bhanuGandham I uploaded multiple times because of the problem with the internet. Now, I have no idea how to delete it since I can't find a deletion buttion