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Illumina / REViewer

A tool for visualizing alignments of reads in regions containing tandem repeats
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[error] Failed to extract reads from the specified region #63

Closed Tintest closed 9 months ago

Tintest commented 9 months ago

Hello,

I get an error message when I try to run REViewer and I don't understand why. All files are present and seem to be complete. I have sorted and indexed my BAM. Thank you by advance for your help.

./REViewer-v0.2.7-linux_x86_64 --reads results/19A5405_realigned_sorted.bam --vcf results/19A5405.vcf --reference /srv/nfs/disnap/NGS/bioInfo/Bases_de_donnees/GRCh37_decoy/GRCh37Decoy.fasta --catalog CSTB.json --locus CSTB --output-prefix results/19A5405
[2023-09-21 15:43:32.147] [info] Loading specification of locus CSTB
[2023-09-21 15:43:32.159] [error] Failed to extract reads from the specified region
cat CSTB.json
[
    {
        "LocusId": "CSTB",
        "LocusStructure": "(CGCGGGGCGGGG)*",
        "ReferenceRegion": "chr21:45196324-45196360",
        "VariantType": "Repeat"
    }
]
samtools view results/19A5405_realigned_sorted.bam chr21:45196324-45196360 | head
NL500104:777:HCM3GAFX5:3:11502:24673:4992       77      chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGCG     IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIIIIIII   XG:Z:CSTB,0,1[12M]2[1M1X61M]
NL500104:777:HCM3GAFX5:3:11401:3971:20320       77      chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCGGCGCTGGTGTCGGGAGGGAGCG     IIIIIIIIIIII!IIIIIIII!II!IIIIIIII!III!IIIIIIIIIIIIII!IIIIIIIIIIIIIIIIII!III   XG:Z:CSTB,0,1[12M]2[1M1X38M1X22M]
NL500104:777:HCM3GAFX5:3:11407:21027:17686      125     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGC     III!IIIIIIIIIIIII!IIIIIIIIIIIIIIIIIIIIIIII!IIIIIIII!IIIIIII!I!IIIIIIII!III!   XG:Z:CSTB,0,1[1S12M]2[1M1X60M]
NL500104:777:HCM3GAFX5:2:11211:22012:2769       125     chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGCG     !I!IIII!IIIIIIII!IIII!IIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIII   XG:Z:CSTB,0,1[12M]2[1M1X61M]
NL500104:777:HCM3GAFX5:2:21211:25239:12812      189     chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCGGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGCG     !I!!II!!IIIIIIIIIIIIIIIIII!III!IIIII!!III!IIIIIIIIIIIII!IIIIII!IIIIIIIIIIII   XG:Z:CSTB,0,1[12M]2[1M1X23M1X37M]
NL500104:777:HCM3GAFX5:2:11202:2727:9211        189     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGC     I!I!IIII!IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!IIIIIIIIIIIIIIIIIIII!IIIIIIIIIII   XG:Z:CSTB,0,1[1S12M]2[1M1X60M]
NL500104:777:HCM3GAFX5:2:21308:17388:5398       125     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGTCGGGAGGGAGC     I!I!IIII!IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!IIIIIII!IIIIIII!IIII!IIIIIIIIIII   XG:Z:CSTB,0,1[1S12M]2[1M1X60M]
NL500104:777:HCM3GAFX5:3:21407:19722:5663       125     chr21 45196325  0  *    *       0       0       CGGGGGGCGGGGCGGGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGT     !I!III!!III!!I!IIII!IIIIIIII!IIIIIIIIIIIIIIIIIIII!III!IIIIIIIIIIIIIIIIIIIII   XG:Z:CSTB,0,1[2M1X9M]1[2M1X9M]2[1M1X49M]
NL500104:777:HCM3GAFX5:1:11102:16995:20161      189     chr21 45196325  0  *    *       0       0       CGCGGGGCGGGGCGCGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTGT     II!IIII!IIIII!!III!!IIIIIIIII!IIIIII!IIIIIIIIIIIIIIIIIIII!III!IIIII!I!IIIII   XG:Z:CSTB,0,1[12M]1[12M]2[1M1X49M]
NL500104:777:HCM3GAFX5:4:21512:6434:14465       125     chr21 45196325  0  *    *       0       0       GCGCGGGGCGGGGCGGGGGGCGGGGAGCCTGGCCACCACTCGCCGCAGGCTGGGTCTCCGCGCCCAGCGCTGGTG     I!IIIIII!IIII!I!IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII!I!IIIIIIIIIIIIIII!II!I   XG:Z:CSTB,0,1[1S12M]1[2M1X9M]2[1M1X48M]
grep -v "#" results/19A5405.vcf
chr21  45196324 .       G       <STR2>  .       PASS    END=45196360;REF=3;RL=36;RU=CGCGGGGCGGGG;VARID=CSTB;REPID=CSTB  GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC     1/1:SPANNING/SPANNING:2/2:2-2/2-2:112/112:184/184:0/0:55.288681
sclamons commented 9 months ago

Hi Tintest,

I don't see anything obviously wrong from a quick look. Can you post the aligned bits of your data so I can try some local debugging (or send to sclamons@illumina.com, if you don't want it public)? If so, do you have a public reference for your exact genome build?

Tintest commented 9 months ago

The problem was solved when I realized that the genome used to produce the alignments and the one used for ExpansionHunter and REViewer were not exactly the same.