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0 variants lifted over but had mismatching reference alleles after lift over

Hi, guys:

I am trying to liftOver a VCF file. Please see my log file below. There does not seem to have an error, but somehow none of my SNPs are lifted over. Can someone please let me know what is wrong here?

Thanks!

Jie

===============================================================================

gatk --java-options "-Xmx6g" LiftoverVcf -R $ref -I A01.b37.vcf.gz -O A01.vcf -C /mnt/d/files/hg19ToHg38.chain --MAX_RECORDS_IN_RAM 50000 --REJECT rejected.vcf --DISABLE_SORT true
Using GATK jar /mnt/d/software_lin/gatk/gatk-package-4.1.4.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6g -jar /mnt/d/software_lin/gatk/gatk-package-4.1.4.0-local.jar LiftoverVcf -R /mnt/d/data/gatk_bundle/hg38/Homo_sapiens_assembly38.fasta.gz -I A01.b37.vcf.gz -O A01.vcf -C /mnt/d/files/hg19ToHg38.chain --MAX_RECORDS_IN_RAM 50000 --REJECT rejected.vcf --DISABLE_SORT true

20:17:23.553 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/d/software_lin/gatk/gatk-package-4.1.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Mon Dec 09 20:17:23 GMT 2019] LiftoverVcf --INPUT A01.b37.vcf.gz --OUTPUT A01.vcf --CHAIN /mnt/d/files/hg19ToHg38.chain --REJECT rejected.vcf --DISABLE_SORT true --MAX_RECORDS_IN_RAM 50000 --REFERENCE_SEQUENCE /mnt/d/data/gatk_bundle/hg38/Homo_sapiens_assembly38.fasta.gz --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
Dec 09, 2019 8:17:24 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
[Mon Dec 09 20:17:24 GMT 2019] Executing as [email protected] on Linux 4.4.0-17763-Microsoft amd64; OpenJDK 64-Bit Server VM 11.0.4+11-post-Ubuntu-1ubuntu218.04.3; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.1.4.0
INFO 2019-12-09 20:17:24 LiftoverVcf Loading up the target reference genome.
INFO 2019-12-09 20:17:54 LiftoverVcf Lifting variants over and writing the output file. Variants will not be sorted.
INFO 2019-12-09 20:17:57 LiftoverVcf Processed 100731 variants.
INFO 2019-12-09 20:17:57 LiftoverVcf 100731 variants failed to liftover.
INFO 2019-12-09 20:17:57 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
INFO 2019-12-09 20:17:57 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.
INFO 2019-12-09 20:17:57 LiftoverVcf liftover success by source contig:
INFO 2019-12-09 20:17:57 LiftoverVcf 1: 0 / 10327 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 10: 0 / 3963 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 11: 0 / 5720 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 12: 0 / 4725 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 13: 0 / 2739 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 14: 0 / 2827 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 15: 0 / 3498 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 16: 0 / 3744 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 17: 0 / 5274 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 18: 0 / 2393 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 19: 0 / 4765 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 2: 0 / 7043 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 20: 0 / 1919 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 21: 0 / 1880 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 22: 0 / 2314 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 3: 0 / 5267 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 4: 0 / 4855 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 5: 0 / 5261 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 6: 0 / 5742 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 7: 0 / 4964 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 8: 0 / 4264 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf 9: 0 / 4148 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf X: 0 / 3093 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf Y: 0 / 6 (0.0000%)
INFO 2019-12-09 20:17:57 LiftoverVcf lifted variants by target contig:
INFO 2019-12-09 20:17:57 LiftoverVcf no successfully lifted variants
WARNING 2019-12-09 20:17:57 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats.
[Mon Dec 09 20:17:57 GMT 2019] picard.vcf.LiftoverVcf done. Elapsed time: 0.56 minutes.
Runtime.totalMemory()=4588568576

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