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HaplotypeCaller on whole genome or chromosome by chromosome: different results
I'm working on targeted resequencing data and I'm doing a multi-sample variant calling with the HaplotypeCaller. First, I tried to call the variants in all the targeted regions by doing the calling at one time on a cluster. I thus specified all the targeted regions with the -L option.
Then, as it was taking too long, I decided to cut my interval list, chromosome by chromosome and to do the calling on each chromosome. At the end, I merged the VCFs files that I had obtained for the callings on the different chromosomes.
Then, I compared this merged VCF file with the vcf file that I obtained by doing the calling on all the targeted regions at one time. I noticed 1% of variation between the two variants lists. And I can't explain this stochasticity. Any suggestion?