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LiftoverVCF; mismatching reference alleles after lift over
I am running LiftoverVCF from gatk-220.127.116.11 to convert my VCF from hg18 to hg19.
Here is my command:
/apps/well/java/jdk1.8.0_172/bin/java -jar /users/mcvean/tutert/gatk-18.104.22.168/gatk-package-22.214.171.124-local.jar LiftoverVcf -I /users/mcvean/tutert/58BC_affy_all.with_chr.vcf -O /users/mcvean/tutert/liftedover.vcf -CHAIN /users/mcvean/tutert/hg18ToHg19.over.chain -REJECT /users/mcvean/tutert/rejected.vcf -R /users/mcvean/tutert/ucsc.hg19.fasta -RECOVER_SWAPPED_REF_ALT true --MAX_RECORDS_IN_RAM 100000 -
However in my output log I see this:
303130 variants lifted over but had mismatching reference alleles after lift over.
42.2971% of variants were not successfully lifted over and written to the output.
I believe this is an alt/ref mismatch problem still (since I looked at the snps in the output rejected file and they were all both in hg18/hg19 but just differed by this mismatch).
Could someone please help me with this?