I am trying to use liftover a vcf file from hg19 to hg38. I don't get any error messages but I do get warning messages that confuse me.
a) GATK version used: gatk-184.108.40.206
b) Exact GATK commands used
c) The entire error log if applicable.
There is no error log but I do get the following warnings:
WARNING 2020-07-06 12:12:45 LiftoverVcf 23454 variants with a swapped REF/ALT were identified, but were not re covered. See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO 2020-07-06 12:12:48 LiftoverVcf Writing out sorted records to final VCF.
WARNING 2020-07-06 12:12:49 SortingCollection There is not enough memory per file for buffering. Reading will be unbuffered.
What do these warnings mean? I am working on SSH. How do I fix the the problem?
Thank you in advance!
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