Yes, "SACE_S288C_v1_chr_01" is the source, but according to the chain file format, the target name is on the 3rd column while the query/source name is on the 8th column, isn't it?
Liftover from one yeast species into another one fails
Hello everyone, I have the vcf of a S. cerevisiae genome mapped against the S. cerevisiae reference and I'm trying to lift over it to the reference genome from S. paradoxus. But no variants are lifted over.
Here are the versions information:
[isedeno@login01 liftover]$ gatk --version
Using GATK jar /opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-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 -jar /opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-local.jar --version
The Genome Analysis Toolkit (GATK) v4.6.2.0
HTSJDK Version: 4.2.0
Picard Version: 3.4.0
The command I used and the obtained output are:
[isedeno@login01 liftover]$ gatk --java-options "-Xmx16g" LiftoverVcf -I ../../../Public/vcalling/YMX005553_SACE.g.vcf -O lifted_over.vcf -C toChain/axtChain/SAPA_YPS138.SACE_S288C.over.chain --REJECT rejected.vcf -R ../../../Public/ymez/data/ref/SAPA_YPS138_v1/fasta/SAPA_YPS138_v1_allChr.fasta
Using GATK jar /opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-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 -Xmx16g -jar /opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-local.jar LiftoverVcf -I ../../../Public/vcalling/YMX005553_SACE.g.vcf -O lifted_over.vcf -C toChain/axtChain/SAPA_YPS138.SACE_S288C.over.chain --REJECT rejected.vcf -R ../../../Public/ymez/data/ref/SAPA_YPS138_v1/fasta/SAPA_YPS138_v1_allChr.fasta
10:01:09.395 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Apr 07 10:01:09 CST 2026] LiftoverVcf --INPUT ../../../Public/vcalling/YMX005553_SACE.g.vcf --OUTPUT lifted_over.vcf --CHAIN toChain/axtChain/SAPA_YPS138.SACE_S288C.over.chain --REJECT rejected.vcf --REFERENCE_SEQUENCE ../../../Public/ymez/data/ref/SAPA_YPS138_v1/fasta/SAPA_YPS138_v1_allChr.fasta --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 --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Tue Apr 07 10:01:09 CST 2026] Executing as isedeno@login01.cluster on Linux 5.14.0-611.36.1.el9_7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.18+8-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.6.2.0
INFO 2026-04-07 10:01:09 LiftoverVcf Loading up the target reference genome.
INFO 2026-04-07 10:01:09 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)
INFO 2026-04-07 10:01:10 LiftoverVcf Processed 316744 variants.
INFO 2026-04-07 10:01:10 LiftoverVcf 316744 variants failed to liftover.
INFO 2026-04-07 10:01:10 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
INFO 2026-04-07 10:01:10 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.
INFO 2026-04-07 10:01:10 LiftoverVcf liftover success by source contig:
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_01: 0 / 15694 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_02: 0 / 25736 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_03: 0 / 8261 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_04: 0 / 28951 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_05: 0 / 12253 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_06: 0 / 12438 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_07: 0 / 24136 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_08: 0 / 21171 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_09: 0 / 13244 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_10: 0 / 27164 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_11: 0 / 15341 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_12: 0 / 21718 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_13: 0 / 18217 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_14: 0 / 21201 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_15: 0 / 28891 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_16: 0 / 16436 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_2m: 0 / 1102 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf SACE_S288C_v1_chr_mt: 0 / 4790 (0.0000%)
INFO 2026-04-07 10:01:10 LiftoverVcf lifted variants by target contig:
INFO 2026-04-07 10:01:10 LiftoverVcf no successfully lifted variants
WARNING 2026-04-07 10:01:10 LiftoverVcf 0 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO 2026-04-07 10:01:10 LiftoverVcf Writing out sorted records to final VCF.
[Tue Apr 07 10:01:10 CST 2026] picard.vcf.LiftoverVcf done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=276824064
Tool returned:
0
When looking online, the error always seemed to be the chromosome names, so I checked that and I dont think that is the error:
[isedeno@login01 liftover]$ grep -e "chr" toChain/axtChain/SAPA_YPS138.SACE_S288C.over.chain | cut -d" " -f8 | sort -u
SACE_S288C_v1_chr_01
SACE_S288C_v1_chr_02
SACE_S288C_v1_chr_03
SACE_S288C_v1_chr_04
SACE_S288C_v1_chr_05
SACE_S288C_v1_chr_06
SACE_S288C_v1_chr_07
SACE_S288C_v1_chr_08
SACE_S288C_v1_chr_09
SACE_S288C_v1_chr_10
SACE_S288C_v1_chr_11
SACE_S288C_v1_chr_12
SACE_S288C_v1_chr_13
SACE_S288C_v1_chr_14
SACE_S288C_v1_chr_15
SACE_S288C_v1_chr_16
SACE_S288C_v1_chr_mt
[isedeno@login01 liftover]$ grep -e "chr" toChain/axtChain/SAPA_YPS138.SACE_S288C.over.chain | cut -d" " -f3 | sort -u
SAPA_YPS138_v1_chr_01
SAPA_YPS138_v1_chr_02
SAPA_YPS138_v1_chr_03
SAPA_YPS138_v1_chr_04
SAPA_YPS138_v1_chr_05
SAPA_YPS138_v1_chr_06
SAPA_YPS138_v1_chr_07
SAPA_YPS138_v1_chr_08
SAPA_YPS138_v1_chr_09
SAPA_YPS138_v1_chr_10
SAPA_YPS138_v1_chr_11
SAPA_YPS138_v1_chr_12
SAPA_YPS138_v1_chr_13
SAPA_YPS138_v1_chr_14
SAPA_YPS138_v1_chr_15
SAPA_YPS138_v1_chr_16
SAPA_YPS138_v1_chr_mt
[isedeno@login01 liftover]$ grep -e ">" ../../../Public/ymez/data/ref/SAPA_YPS138_v1/fasta/SAPA_YPS138_v1_allChr.fasta
>SAPA_YPS138_v1_chr_01
>SAPA_YPS138_v1_chr_02
>SAPA_YPS138_v1_chr_03
>SAPA_YPS138_v1_chr_04
>SAPA_YPS138_v1_chr_05
>SAPA_YPS138_v1_chr_06
>SAPA_YPS138_v1_chr_07
>SAPA_YPS138_v1_chr_08
>SAPA_YPS138_v1_chr_09
>SAPA_YPS138_v1_chr_10
>SAPA_YPS138_v1_chr_11
>SAPA_YPS138_v1_chr_12
>SAPA_YPS138_v1_chr_13
>SAPA_YPS138_v1_chr_14
>SAPA_YPS138_v1_chr_15
>SAPA_YPS138_v1_chr_16
>SAPA_YPS138_v1_chr_mt
[isedeno@login01 liftover]$ grep "contig" ../vcfs/YMX005553_SACE.nuclearFinal.vcf
##contig=<ID=SACE_S288C_v1_chr_01,length=230218,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_02,length=813184,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_03,length=316620,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_04,length=1531933,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_05,length=576874,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_06,length=270161,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_07,length=1090940,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_08,length=562643,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_09,length=439888,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_10,length=745751,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_11,length=666816,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_12,length=1078177,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_13,length=924431,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_14,length=784333,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_15,length=1091291,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_16,length=948066,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_mt,length=85779,assembly=SACE_S288C_v1_allChr.fasta>
##contig=<ID=SACE_S288C_v1_chr_2m,length=6318,assembly=SACE_S288C_v1_allChr.fasta>
I created my own chainfile using the DoBlastzChainNet.pl script, although I didnt run the complete pipeline, I ran it until obtaining the chain file (SAPA_YPS138.SACE_S288C.over.chain). Maybe the chain file is the problem?
I really dont know what could be wrong, so any help would be apreciated.
1 answer
I think there is a misunderstanding in the chain file: the source/target are swapped.
if the ''rejected.vcf" contains a chromosomes named "SACE_S288C_v1_chr_01" , so "SACE_S288C_v1_chr_01" is the SOURCE. It should be found in the source of the chain file, the 3rd colum. But in your chain file , it's in the target (8th) column.
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Pierre Lindenbaum
I just ran the chainSwap command from kentutilities to invert the target and query from the chain files. And then used the exit to run the liftover again and it worked!!!
[isedeno@login01 liftover]$ gatk --java-options "-Xmx16g" LiftoverVcf -I ../vcfs/YMX005553_SACE.nuclearFinal.vcf -O lifted_over.vcf -C toChain/axtChain/SACE_S288C.SAPA_YPS138.over.chain --REJECT rejected.vcf -R ../../../Public/ymez/data/ref/SAPA_YPS138_v1/fasta/SAPA_YPS138_v1_allChr.fasta
Using GATK jar /opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-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 -Xmx16g -jar /opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-local.jar LiftoverVcf -I ../vcfs/YMX005553_SACE.nuclearFinal.vcf -O lifted_over.vcf -C toChain/axtChain/SACE_S288C.SAPA_YPS138.over.chain --REJECT rejected.vcf -R ../../../Public/ymez/data/ref/SAPA_YPS138_v1/fasta/SAPA_YPS138_v1_allChr.fasta
14:35:40.990 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/opt/apps/gatk/4.6.2.0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Tue Apr 07 14:35:41 CST 2026] LiftoverVcf --INPUT ../vcfs/YMX005553_SACE.nuclearFinal.vcf --OUTPUT lifted_over.vcf --CHAIN toChain/axtChain/SACE_S288C.SAPA_YPS138.over.chain --REJECT rejected.vcf --REFERENCE_SEQUENCE ../../../Public/ymez/data/ref/SAPA_YPS138_v1/fasta/SAPA_YPS138_v1_allChr.fasta --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 --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Tue Apr 07 14:35:41 CST 2026] Executing as isedeno@login01.cluster on Linux 5.14.0-611.36.1.el9_7.x86_64 amd64; OpenJDK 64-Bit Server VM 17.0.18+8-LTS; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.6.2.0
INFO 2026-04-07 14:35:41 LiftoverVcf Loading up the target reference genome.
INFO 2026-04-07 14:35:41 LiftoverVcf Lifting variants over and sorting (not yet writing the output file.)
INFO 2026-04-07 14:35:42 LiftoverVcf Processed 103716 variants.
INFO 2026-04-07 14:35:42 LiftoverVcf 5795 variants failed to liftover.
INFO 2026-04-07 14:35:42 LiftoverVcf 52860 variants lifted over but had mismatching reference alleles after lift over.
INFO 2026-04-07 14:35:42 LiftoverVcf 56.5535% of variants were not successfully lifted over and written to the output.
INFO 2026-04-07 14:35:42 LiftoverVcf liftover success by source contig:
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_01: 1091 / 3441 (31.7059%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_02: 3226 / 8796 (36.6758%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_03: 1052 / 2260 (46.5487%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_04: 5038 / 10131 (49.7286%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_05: 2197 / 4399 (49.9432%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_06: 1136 / 2957 (38.4173%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_07: 3976 / 8718 (45.6068%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_08: 1767 / 5952 (29.6875%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_09: 1988 / 4091 (48.5945%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_10: 2951 / 9696 (30.4352%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_11: 2929 / 5685 (51.5215%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_12: 3879 / 7912 (49.0268%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_13: 3414 / 6951 (49.1152%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_14: 2779 / 6337 (43.8536%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_15: 4632 / 10338 (44.8056%)
INFO 2026-04-07 14:35:42 LiftoverVcf SACE_S288C_v1_chr_16: 3006 / 6052 (49.6695%)
INFO 2026-04-07 14:35:42 LiftoverVcf lifted variants by target contig:
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_01: 1082
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_02: 3169
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_03: 1055
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_04: 5002
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_05: 2177
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_06: 1164
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_07: 4012
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_08: 1765
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_09: 1946
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_10: 2945
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_11: 2938
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_12: 3932
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_13: 3521
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_14: 2776
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_15: 4618
INFO 2026-04-07 14:35:42 LiftoverVcf SAPA_YPS138_v1_chr_16: 2959
WARNING 2026-04-07 14:35:42 LiftoverVcf 44751 variants with a swapped REF/ALT were identified, but were not recovered. See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO 2026-04-07 14:35:42 LiftoverVcf Writing out sorted records to final VCF.
[Tue Apr 07 14:35:42 CST 2026] picard.vcf.LiftoverVcf done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=243269632
Tool returned:
0
I guess now I will make a proper chain file to run everything, thanks!!!
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please what is the output of :
show us a few variants of the 'rejected.vcf'
This is the output from the grep:
And this are some variants from the rejected.vcf:
All variants are marked as "NoTarget":
EDIT: The original vcf was filtered, so it contains only biallelic snps, in case that helps.