unparsable vcf record

[valeandri]

Hi,

I am loading this VCF using IGV and when jumping to chr3 I get this error:

SEVERE [Dec 12,2025 09:20] [FeatureTrack] htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 1699441: unparsable vcf record with allele CTGATTAACCACTTGGAAATTCTGCAATAAGAGAGTTTCAAAACTGCTCTATGAAAGGAAGGTTCAACTCTGTGAGTTGAAAGCACACGTCACAAAGAAGTTTCTGAGAACTCTTCTGTCTAGTTTTAAATGAAGAAGTCACGTTTCAAACGAAGGCCACAAAGAGGTCCAAATATCCACCAGCAGATTCTATAAAAAGAGTGTTGCGAAACTGCTCTCTCAAGAGGAATGCTCAATTCTGTGTGTTGAATGCAAATATCACAAAATAGTTTCCGACAATGCTTCTGTCAAGTATCTATTTGAAAATATTTCCTTTTCTACCGTAGACTTCAAAGCAGTCTAAATGTACACTTGGATATTCCACAAAATAATGTTTCAAAACTGCTCTATTAAAAGAAACGTTAACATTTGTAAGGTTAATGCACACATCACAAAGTAATTTCTGAAAATGATTCTGTCCAGTTTTTCTATGAAGATATTTCCTTTTCTACCACAGCCTCAAACTGCTGTAAATATCCACCTGGAAATTCTAAAAAAAGAGTGTTTCAAAACTGCTCTATCGAAAGGAAGTTTTAACTCTGTGAGTTGAATGCACACATGACAAAGATGTTTCTGAGAATTCTTCTGTCCAGTTTTATTTGAAGGAATTCCATTTCCAACGCAGACCTCAACAAGTCCAAATATTAACTTGCAGATTCTACAAATAGTGTGTTTCAAAACTGCTCTATCAAAAGAAAGATTAAACTCTGTGAATTGAACGCACACATCACAAAGTAGTTTCAGAGAATCATTCTCTCTAGTTTTCCTATGAAGATATTGCCTTTTCTAAAATTGGCCTCTAACGGTGCTAAATATCCACTAGGAAATTATACAAAAATAGTGTTTCAGAACTGCTCCATACAAAGGAAAGTACAACTCGGTGAGTTGAAAGCACACATCACAAAGAATTTCTGAGAACTATTCTTTCTAGTTTTATATGCAGAAATAACTTTTCAAACGAAGGCCACAAAAAGGTCCAAATATCCACTTGCATATTCTACAAAAAAAGAGTTTCAAAACTGCTCTATGAAGAGCAATGTTCAACACTGTGAGTTGAATGCAAATATTGCGAATTAGTTTCTGACAATGCTTCTGTCTAATTTTTATGTGAAGTTATTTCCTTTTCTACCGTAGGCCTCAAAGCCCTCTGAATGTACACTTCCAAATATCACAAAAAGAGTGTTTCAAAACTGCTCTGTCAAAGGAATGGTTAAACATTGTAAGCTGAATGCACCCATCACAAAGTAGTTTCTGAGAATGATTCTGTCTAGTTTTTTAATGAAAATATTCCCTTTTCAATCATTGGCCTCAAACCACTCAAAATATCCACTTGGAAATTCTACAAAAAGATTATTTCAAAAGTGCTCTATCGAAAGGAAGTTTCGACTCTGTGTGTTGAATGCACACATCACAAAGAAGTTTCTGAGAATTCTTCTGACAAGTCTTATATGAAGAAATCCCATTTCCAAAGAAGGCCTCAAAAAAGTCCAAATATTCACTTGCAGATTCTACAAAAAGATTGTTTCAAAACTGCTCTATCAACAGAAAGGTTAAACCCTTTTGATTTGGACGCACACCTCACAAAGAAGTTTCTGAGAATTCTTCTGTCTAGTTTTATATGAAGAAATCACTTTTCAAAAGAAGGCCACAAGGAGGTCCCAAAATCCCCTTGTAGATTCTACAAAAAGAGTGTTTCAAAACTGCTCTATCAAGAGGAATGTTCAACTCTGTGAGTTGAATGCAAATATCACATAGTAGTTTCTGACAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCCACCGTAGGCCTCAAAGCACTCAAAATATACACTTGCAATTTCCACAAAAAGAGTGTTTCAAAACTGTTCTATGAAAAGAAAGGTTAAACTCTGTAAGCTGAATGCGCCCATCACAAAGTAGTTTCTGAGAATGATTCTGTCTAGATTTCAATGAAGATATTTCCTTTTCTACCATACGCCTCAAACCGCTCTAAATAATATCCACTTGGAAATTCTACAAAAACAGTACTTCAAAACTGCTCTATGGAAAGGAAGGTTCAACTCTGTGAGTTCAATGCGCACATCACAAAGAAGTGTCTGCGAATTCTTTTGTCAAGTTTTATATGAAGAAATCCCGTTTCCAACTAAGGCCGTAAAAAAGTCCAAATATTCCCTTGCAGATGCTACAAAAAGTGTGTTTCAAAACTGCTCTATCAAAAGAAAGGTTAAATTCTCTGAATTGAACGCAGACATCAAAAAGTAGTTTCTGAGAATCATTCTGTCCAATTTTTTTATGAAGATATTGCCTTCTCTACCATAGGCCTCAAACGGTGCCAAATATACACTGGGAAATCCTAAAAAAAAAGAGAGTGTGAAAACTGCTCCATCGAAAGGAAGTTTCAACCCTTTGAGTTGAAAGCACACATCACAAATATGTTCCTCAGAATTCTTCTGTCTATTTTTATATGAAGAAACCACGTTTCAAAAGTACGCCACAAGGTGGTACAAATATCCACTTGCAGATTCTACAAAAAGAGTGTTTAAAATCTGCTCCATGAAGAAGAATGTTCAACTCTGTGAGTTGAATGCTAATATCACAAAGTAGTTTCTGACAAAGATTCTGTCTAGTTTTTATGTAAAGATATTTCCTTTTCTATCGTAGGCCTCAAATCGCTCTAAATATACACTTGCAATTTCCACAAACAGAGTGTTCCAAAACTGCTCTAAAAAAGAAAGGTTCAACTCTGTGAGCTGAATGCACACATCACAAAGTAGTTTCTGAGAATGATTCTGACTAATTTTTCTTCGCAGATATATCCTTTTCTACTGTACGCCTCAAACGGCTCTAGATATCCACTTGGAAATTCTAAAAAAAGAGTATTTCAAAACTGCTCTATCGAAAGGAAGGTTCAACTCTGTGAGTTGAAAGCACACATCACAAAAAAGTTCCTCACAATTCTTCTGTCTAGTTTTATATGAAGAAATCACTTTTCAAAGGAAGGCCACAAACAGGTCCAAATATCCACTTGTATTTTCTACAAAAAGAGTGTTTCAAACTGCTCTATCAAGAGGAATGTTCAACTCTGTGAGTTGAATGCAAATATCACAAAGTAGTTTCTGACAATGCTTCTGTCTTGTTTTTATGTGAAGATATTACCTTTTCTACAGTAGGCCACAAAGCGCTCTAAATATACACTTGCAAATTCCACAAAAAGAGTGTTTCAAATCTGCTCTATGAAAAGAAAGGTTAAACTCTGTGAGATGAATGCACACATCACAAAGAAGTGTCTGAGAATTCTTCTGACAAGTCCTATATGAAGAAATGCCGTTTCCAATGATGGCCTCAAAAAAGTCCAATTATTCACCTGCAGATTGTACAAAAAGAGTGTTTTCAATACTGCTTCTATAAAGGAAAGGGTAAACTTTGTGCGTTTGAATGCACACATCACAAATAAGTTTCTGAGAATCATTCTCTCTTGTTTTTCTGTGAAGWTATTGCCTTTTCTACCATAGGCCTCAAAAGGGGCTAAATATCCACTTGGATACCCCACTAAAAGAGAGTTTCATAACTGCTGTATCGAAAGGAAGTTTCAGCTCTGTGAGTTGAAAGCACACGTAACAAAGAAAGAAGTTTCTGTGAATTCTTCTGTCTTGTTTTACATGAAGAAATCACGTTTCAAATGAAGGCCACATAGAGGTCCAAATATCCACTTACAGATTCTACAAAAAGAGTGTTTCAGTATTCCTCTATCGAAAGCAAAGTTAAACTCTGTGAGTTGAATACACACATCACAAAGTAGTTTCTGAGAATCATTCTGTCTGGTTTTTCTATGAAGATATTGCCTTTTCTACCATTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTAAACTCTGTGAGTTGAATACACACATCACAAAGTAGTTTCTGAGAATCATTCTGTCTGGTTTTTCTATGAAGATATTGCCTTTTCTACCATAGGCCTCAAATGGCACTAAATATCCACTTGGAAATCCTACAAAAAGAGAGTTTCCAAACTGCTCTATCAAAAGAAAGGTTCAACTCTGAGAGTTGAAATCACACATCACAAAGAAGTTTCTGAGAATTCTTCTGTCCAGTTTTATATGATGAAATCACCTTTCAAAGGAAGGCCACAAAGAAGTCCAAATATCCACTTGCAGATTCTACAAAAATAGTGTTTCAAAACTGCTCTATCAGGAGGAAGGTTCAACTCTGTGAGTTGAATGCCAATATCACAAAGTAGTTTCTGACAATGCTTCTGTCTAGTTTTAATGTGAAGATATTTCCTTTTCTACAGTAGGCCTCAAAGCGCTCTAAATATACACTTGAAAATTCCACAAAAATAGTGTTACAAAACTACTCTACCACAGGAAAGGTTAAACTCTGTAAGCTGAATGCACACATAACTAATTAGTTTCTGAGAATGATTCTGTCTAGGTTTTGTATGAAGATATTTCCTTTTCTTCCATAGGCATCTATCCGCTCTAAATATCCACTTGGAAATCCTACAAAAAGAGTATTCCAAAACTGCTCTATCATAAGGACGGTTCAACTCTCTGGGTTGAACGCACACATGAAAAAGAAGTTTCTGAGAATTCTTCTGCCAAGTTTTATATGAAGAAATGCCGTTTCCAACGAACGCCTCATAAAAGTGTAAATATTCAATTGCAGATTCTGCAAAAAGAGTGTTTTAAAACTGCCGTATGAAAAGAAAGTTTAAATACTGTGAGTTGAACGCACACAGCACAAAGCAGTTTCTGAGTATCATTCTGTCTTGTTTTTATGTGATGATATTTCCTTTTCTACCGTAGGCCTCAAACGGCGCTAAATAGCCACTTGGAAATTCTACAAAAAGAGTATTTCAGAACCGCTCTATCGAAAGGAAGGTTCAACACTGTGAGTTGAAAGCACACATCACAAAGTAGATTCTGATAATTCTTCTGTCAAGTTTTATATGAAGAAACTCCATTTTCAAAAATGGCCTCTAAAAAATCCAAATATTCACTTGCAGATTCTACAAAAAGAGTGTTTAAAAACTGCTCTATCAAAAGAAAGGTTAAACTCTGTGAGTTGAATGCACACATCACAAAGTAGTTTCTGAGAATCTTTCTGTCTAGTTTTTCTATGAAGATACTGCCTTTTATTCCATCGGCCTCAAACGGCGCTAAATATCCACCTGGAAATTCTACAAAAAGAGAGTATCAAAACTGCTCTATCGAAAGAAATGTTCAACACTGTGAGTTGAATGCAGATATCACAAAGTAGTTTCTGACTATGCTTCTGTCTAGTTTTAATGGGAAGATATTTCCTTTTCTACCATAGGCCTCAAAGCGCTCTAAATATACACTTGCAAAGTCCACAAAAAGAGAGTTACAAAACTGATCTATCAAAAGAAAGGTTAAAGTCTGTAAGCTGCATGCACACATTAGAAAGTAGTTTCTGAGAATGATTCTGTCTAGGTTTTCTATGAAGATAATTCCTTCTCTACCACAGGCCCCAAACGGCTCTAAATATCCACTTGGAAATCCCACAAAAAGAGTATTTCAAAACTGCTCTATCAAAAGGAACGTTGACCTCTGTGAATTGAATGCACAGATCACAAAGAAGTTTCTGAGAGTTCTTCTCTCAAGTTTTCTGTGAAGAAATCCCGTTTCCAAAGAAGGCCTCCAAAAAGTACAAATATTCACTTCCAGATTCTACAAAAAGACTGTTTCAAAAAAGCTCTATCAAAAGAAAGTTTAAACTCTGTGAGTCGTAAGCACACATCACAAAGAAGTTTCTCAGAATCATTCTGTCTATTTTTTCTAACAAGATATTTCCTTTTCTAGCATAGGCCTCAAATGGAGCTAAATATCCACTTGGAAATACTACAAAAAGAGTTTCAAAACTGCTCTATCGAAAGAAAGGTTCAACTGTATGAGTTGAAAGCACACATCACAAAGAAGTTTCTGAGAGTTCTTCTGTCTAGTTTTGTATGAAGAAATCAGGTTTGAAATGAAGGCCACAAAGAGGTTCAAATATCCACTTGCAGATTCTACAAAAAGAGTGTTTCAAAACTGCTCTATCAAGAGAAATCTTCAACTCTGTGGGTTGAATGCAAATATCCCAAAGTAGTTTCTGACAATGCTTCTGTCTGGTTATTACGTGAAGATATATCCTTTTCTACCATAGGCCTCAAAGGGCTCTAAATAAACACTTCCAAAATCCACAAAAAGAGTGTTTCAAAACTGCTCTATCAATCAAAAGAAAGGTTAAACTCTGTAAGCTGAATGCACACATCACAAAGTAGTTTCTGAGAATGATTCTGTCTCGTTTTCCTATGAAGATATTTCCTATGAAGATATTTCCTTTCCTATCACAAGCCTCAAAGCGCTCTAAATATCTACTTGGAAATTCTACAGAAAGAGTATTTCAAAACTTCTCTCTCGAAGGGAAGGTTCAACTCTGTGAGTTGAATGCCCACATCACAAAGTAGTCTCTGAGAATTCTTCTGTTAAGTTTTATTTGAAGAAATCCCTTTACCAACGAACGCCACAAAAATTCCAAATATTCACTTGCAGATTCTCCAAAAAGAGTGTTTCAAAACTATTCTATAAAAAGAAAGTTTAACACTGTGAGATGAATGCACACATCTTAAAGTAGTTTCTGACAATCATTCTGTCTAGTTTTTCTATGAAGATATTGCCTTTTCTACCATAGGCCTCAAACGGCACTATATATCCACTTGGAAATTGTACAAAAAGAGCGTTTACAAACTGCTCTACCGAAAGGAAGGTTCAACACTGTGAGTTGAAAGCACACATCACAAAGATGTTTCTGAGAATTCTTCTGTTTAGTTTTATATGAAGAAACCACGTTTCAAACGAAGGTCACAAAGAGGTCCAAATATGCACGTGCAGATTCTACAAAAATAGTGTTTCAAAACTGCTTTATCAAGAGGAACGTTCAACTCTGTGAGTTCAATGCAAATGTCACAAAGAAGTTTCTGACAATGTTTCTGTCTAGGTTTTAGGTGAAGATATTTCCTTTTCTAACGTAGGCTGCCGAGCACTCTAAATATACACTTGCAAAATTCCACAAAAAGAGTGTTTCAAAACTGCACAATCAAAAGAAAGGTTAAACACAGTAAGCTGAATGCACACGGGACAAAGTAGTTTCTGAGAAGGATTCTGTCTTGTTTTTCTACGAAGATATGTCCTTCTCCAAAATAGGCCGCAAACCGCTCTAAATATTCACTTGGAATTTCTACAAAAAGAGTATTTCAAAACTGCTCTATCGAAAGGAAGGTTCAAACCTGTGAGTTGAATGCACATATCACAAAGAAGGTTCTGAGAATTCTTCTGTCAAGTTTTATGTGAAGAAACCCCGTTTCCAACGAAGGCCTCTTAAAAGTCCAAATATTCACTTGCAGATACTACAAAAACACTGTTTCAAAAGTGCTCTATCAAAAGAAAGTTTAAACTGTTTGAGTTGAACGCACACTTCACAAAGTAGTTTCTGAGAATCGTTATGTCAAGTTTTCCTAAGAAGATATTACCTTTTCAACCATAGGCCTCAAACAGCCCTAAATATCCACTTGGACATTCGACAGAAAGAGAGTTTCAAAACTCCTCTTTCGAAAGGCATGTTCCGTGAGTTGAACACAAACATCACAAGGTAGTTTCCGATAATCATTCTGTCTAATTTTTCTATGATGATAATGCCTTTTCTACCATTGGCTTCAAACGGCGCTAAATATCCACTTGGAAATTCTACAAAAAGAGTGTTTCAAAATTGCTCTATGAAGAGGAATGTCCAGCTCTGTAAGTTGAATGCAAATATCACAAATTAGTTTCTGACAATGCTTCTTTCTGGTTTTTATGTGAAGATATTTCCTTTTCTACCACAGGCCTCAAAGCGCTCTAAATATACACTTGCAAATTCCACAGAAAGAGTGTTTGAAAACTGCTGTATCAAAAGAAAGTTAAACTCTGTAAGCCGAATGCAGACATCACAAAGCAGTTTCTGAGAATGATTCTGTCTAATTTTTCTATGAAGATATTTCCTTTTCAACCACAAGCCTGAAACCGCTCTAAATATGCATTTGAAATTCTACAAAAAGAGTATATCAAAACTGCTCTATGGAAAGGAAGGTTAAACTCTGTGAGATGAATGCACTCATCACAAAGAAGTTTCTGAGAATTCTTTGGCAAAGTTTTATATGACAAAATCCCTTTTCCAAAGAAGGCCACAAAAATGTCCAAATATTCACTTGCAGATCCTCCAAAAAGTGTGTTTCAAAACTGCCCTATCAAAAGAAAGTTTGAACTCAGTGAGTTGAATGCACACATCACAAAGCAGTTTCTGAGAATCATTCTGTCTAGTTCTTCTATGAAGATATTGCCTTTTCTACCATAGACCTCAAACGGCGCTAAATATCCACTTGGAAATTCTACAAAAAGAGAGCTTCAAAACTGCTTTATCGAAAGGAATGTTAAAATATGTGAGTTGAAAGCACACATCACAAAGAAGTTTCTGAGAATTCTTCTGTCTAGTTTTATATGAAGAAATCACGTTTCAAACGAAGGCCCCAAAGAGGTCCAAATATACACCTGCAGATATTACAAAAAGAGTGTTTCAAAACTGCTCTATCATAAGAAAGGTTAAACTCTGTAAGCTTAATGCAAACATCACAAAGTAGTTTCTGAGAATGATTCTGTCTAGTTTTTCTATGAAGATATTTAATTTTCTGCCATAGGCCTCAAACCGCTCTAAATATACACTTGGAAATTCTACAAAAAGAGTATTTTAAAACTGCTCTATCGAAAGGAAGTTTTAACTCTGTGAGTTCAATGCACACATCAGAAAGAACTTTCTGAGAATTCTTCTGTCAAGTTTTAAAAGAAGAAAACCCGTTTCCAACAAAGGCCTCAAATATGTAAAAATATTAATTGGCACATTCAACAAAAAAGAGTGTTTCAAAACTGCTCCATCAAGAGGAACGTTCAACTCTGTGAGTTGAATGCAAATATCACAAAGTAGATTCTGACAATGCTTCTGTCAAGTTTTTATATGAAGATATTTCCTTTTCTACCATAGGATTCAAAGCGCTCTAAACATCCACTTGGAAATTCTACAAAAAGAGTGTTTCAAATCTGCTCTATCAAAAGGAAGGTTGCACTCTGAGAGTTGAATCCACACATCCCAAAGAATTTTCTGAGAATTCTTCTGTCTAGTTTTATACGAAGAAATCCTGTTTCCACTGAAGGCCTCAAAGAGTTCCAAACATACACTTGCAGAAACTACAAAAAGAGTGTTTCAAAACTGCTCTATCAAGAGGAATGTTCAACTCCGCGAGGTGAATGCAAACATCACAAAGCAGTTTCTGAGAATGCTTCTGTCTAGTTTTTATGTGAAGATATTTCCTTTTCTACCGTAGGCCTCGAAGTGATCTAAATATCCACTTGCAAACACTACAAAAGGGTGTTACAAAACTGCACTATCAAATGAAGGTTCACCTCTGTGAGTTGAGTACAGACATCACAAAGA, for input source: /home/valentina/Downloads/98b92b86-6efd-421e-85fe-524e5529c59c.vcf.gz
	at htsjdk@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.generateException(AbstractVCFCodec.java:887)
	at htsjdk@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.checkAllele(AbstractVCFCodec.java:678)
	at htsjdk@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.parseAlleles(AbstractVCFCodec.java:640)
	at htsjdk@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.parseVCFLine(AbstractVCFCodec.java:443)
	at htsjdk@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.decodeLine(AbstractVCFCodec.java:384)
	at htsjdk@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:328)
	at htsjdk@4.1.2/htsjdk.variant.vcf.AbstractVCFCodec.decode(AbstractVCFCodec.java:48)
	at org.igv/org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:69)
	at org.igv/org.broad.igv.feature.tribble.VCFWrapperCodec.decode(VCFWrapperCodec.java:43)
	at htsjdk@4.1.2/htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:173)
	at htsjdk@4.1.2/htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:205)
	at htsjdk@4.1.2/htsjdk.tribble.TabixFeatureReader$FeatureIterator.next(TabixFeatureReader.java:149)
	at org.igv/org.broad.igv.feature.tribble.TribbleReaderWrapper.query(TribbleReaderWrapper.java:61)
	at org.igv/org.broad.igv.track.TribbleFeatureSource$IndexedFeatureSource.getFeatures(TribbleFeatureSource.java:226)
	at org.igv/org.broad.igv.track.FeatureTrack.loadFeatures(FeatureTrack.java:723)
	at org.igv/org.broad.igv.track.FeatureTrack.load(FeatureTrack.java:676)
	at org.igv/org.broad.igv.ui.IGV.lambda$repaint$16(IGV.java:2283)
	at java.base/java.util.concurrent.CompletableFuture$AsyncRun.run(CompletableFuture.java:1804)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:840)

Here are the software specifications:
INFO [Dec 12,2025 09:14] [Main] Startup IGV Version 2.18.4 10/03/2024 09:12 AM
INFO [Dec 12,2025 09:14] [Main] Java 17.0.17 (build 17.0.17+10-Ubuntu-122.04) 2025-10-21
INFO [Dec 12,2025 09:14] [Main] Java Vendor: Ubuntu https://ubuntu.com/
INFO [Dec 12,2025 09:14] [Main] JVM: OpenJDK 64-Bit Server VM
INFO [Dec 12,2025 09:14] [Main] OS: Linux 6.8.0-87-generic amd64

Is this due to the "Ns" or to other allele features?

Thanks,
Valentina

[jrobinso]

Hi, honestly I don't know. Have you looked at the VCF specification to see if "N" is allowed there?

If you can create and share a VCF with this record I'll see if I can dig out more information.

[valeandri]

Hi @jrobinso ,

According to the VCF v4.2 specifications, Ns are allowed:

ALT - alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to
be called in any of the samples. Options are base Strings made up of the bases A,C,G,T,N,, (case insensitive)
or an angle-bracketed ID String (“”) or a breakend replacement string as described in the section on
breakends. The ‘’ allele is reserved to indicate that the allele is missing due to a upstream deletion. If there
are no alternative alleles, then the missing value should be used. Tools processing VCF files are not required
to preserve case in the allele String, except for IDs, which are case sensitive. (String; no whitespace, commas,
or angle-brackets are permitted in the ID String itself)

Digging into the issue further, I discovered it might be a problem with the concordance between the ALT allele and the reference sequence at that position. I solved it using bcftools norm. I hope this could be useful to others.

Valentina

[jrobinso]

Thanks for the update.