Question - RealignerTargetCreator : incompatible contigs

Question

[sd6471]

I have question. I do not understand why GATK-RealignerTargetCreator is not working. I downloaded the vcf file from hg38 bundle which is supported by GATK(https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1).

To resolve this, I confirmed the files - vcf and hg38.fa(even dbNSP), and all files use 'chr+N' names. I also tried to do the method in COSMIC vcf file compatibility for Mutect2, but it does not work.

Does anyone have good solutions?

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(I am using the GATK 3.7 version.)

java -Xmx20g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R hg38.fa -I sample_dedup.bam -known Mills_and_1000G_gold_standard.indels.hg38.vcf -o sample.intervals

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ERROR MESSAGE: Input files Mills_and_1000G_gold_standard.indels.hg38.vcf and reference have incompatible contigs. Please see https://software.broadinstitute.org/gatk/documentation/article?id=63for more information. Error details: The contig order in Mills_and_1000G_gold_standard.indels.hg38.vcf and reference is not the same; to fix this please see: (https://www.broadinstitute.org/gatk/guide/article?id=1328), which describes reordering contigs in BAM and VCF files..

ERROR Mills_and_1000G_gold_standard.indels.hg38.vcf contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chr1_KI270706v1_random, chr4_GL000008v2_random, chr14_GL000009v2_random, chr14_KI270726v1_random, chrUn_KI270742v1, chr1_KI270766v1_alt, chr7_KI270803v1_alt, chr8_KI270811v1_alt, chr8_KI270821v1_alt, chr14_KI270846v1_alt, chr15_KI270850v1_alt, chr17_KI270862v1_alt, chr17_KI270857v1_alt, chr22_KI270875v1_alt, chr22_KI270879v1_alt, chr2_KI270894v1_alt, chr17_KI270909v1_alt, chr19_KI270938v1_alt]

ERROR reference contigs = [chr1, chr10, chr11, chr11_KI270721v1_random, chr12, chr13, chr14, chr14_GL000009v2_random, chr14_GL000225v1_random, chr14_KI270722v1_random, chr14_GL000194v1_random, chr14_KI270723v1_random, chr14_KI270724v1_random, chr14_KI270725v1_random, chr14_KI270726v1_random, chr15, chr15_KI270727v1_random, chr16, chr16_KI270728v1_random, chr17, chr17_GL000205v2_random, chr17_KI270729v1_random, chr17_KI270730v1_random, chr18, chr19, chr1_KI270706v1_random, chr1_KI270707v1_random, chr1_KI270708v1_random, chr1_KI270709v1_random, chr1_KI270710v1_random, chr1_KI270711v1_random, chr1_KI270712v1_random, chr1_KI270713v1_random, chr1_KI270714v1_random, chr2, chr20, chr21, chr22, chr22_KI270731v1_random, chr22_KI270732v1_random, chr22_KI270733v1_random, chr22_KI270734v1_random, chr22_KI270735v1_random, chr22_KI270736v1_random, chr22_KI270737v1_random, chr22_KI270738v1_random, chr22_KI270739v1_random, chr2_KI270715v1_random, chr2_KI270716v1_random, chr3, chr3_GL000221v1_random, chr4, chr4_GL000008v2_random, chr5, chr5_GL000208v1_random, chr6, chr7, chr8, chr9, chr9_KI270717v1_random, chr9_KI270718v1_random, chr9_KI270719v1_random, chr9_KI270720v1_random, chr1_KI270762v1_alt, chr1_KI270766v1_alt, chr1_KI270760v1_alt, chr1_KI270765v1_alt, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt, chr1_KI270764v1_alt, chr1_KI270763v1_alt, chr1_KI270759v1_alt, chr1_KI270761v1_alt, chr2_KI270770v1_alt, chr2_KI270773v1_alt, chr2_KI270774v1_alt, chr2_KI270769v1_alt, chr2_GL383521v1_alt, chr2_KI270772v1_alt, chr2_KI270775v1_alt, chr2_KI270771v1_alt, chr2_KI270768v1_alt, chr2_GL582966v2_alt, chr2_GL383522v1_alt, chr2_KI270776v1_alt, chr2_KI270767v1_alt, chr3_JH636055v2_alt, chr3_KI270783v1_alt, chr3_KI270780v1_alt, chr3_GL383526v1_alt, chr3_KI270777v1_alt, chr3_KI270778v1_alt, chr3_KI270781v1_alt, chr3_KI270779v1_alt, chr3_KI270782v1_alt, chr3_KI270784v1_alt, chr4_KI270790v1_alt, chr4_GL383528v1_alt, chr4_KI270787v1_alt, chr4_GL000257v2_alt, chr4_KI270788v1_alt, chr4_GL383527v1_alt, chr4_KI270785v1_alt, chr4_KI270789v1_alt, chr4_KI270786v1_alt, chr5_KI270793v1_alt, chr5_KI270792v1_alt, chr5_KI270791v1_alt, chr5_GL383532v1_alt, chr5_GL949742v1_alt, chr5_KI270794v1_alt, chr5_GL339449v2_alt, chr5_GL383530v1_alt, chr5_KI270796v1_alt, chr5_GL383531v1_alt, chr5_KI270795v1_alt, chr6_GL000250v2_alt, chr6_KI270800v1_alt, chr6_KI270799v1_alt, chr6_GL383533v1_alt, chr6_KI270801v1_alt, chr6_KI270802v1_alt, chr6_KB021644v2_alt, chr6_KI270797v1_alt,.........]

[MatthewP]

Hey, how did you modify VCF files' chr name? I would recommend use _bcftools_ annotate command instead of by-hand.

[sd6471]

I did not modify the file. It has inherently used the chr name. Thus, I do not understand this problem.

Answer 1

[Pierre Lindenbaum]

The gatk error message is quite clear. your dictionaries (@SQ lines in the BAM header and the ##contig= lines in the VCF header) should be the very same, in the same order, and all contigs in a dictionary must be present in the other dictionary (eg see chr11_KI270721v1_random)

but it looks like your BAM don't have the same dictionary [chr1, chr10, chr11, ... as in the file Mills_and_1000G_gold_standard.indels.hg38.vcf

[sd6471]

Thanks. I am confirming the files.