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Where to find hg38 panel-of-normals and germline VCFs without 'chr' prefix?

I’m currently performing somatic variant calling with Mutect2 using hg38 as the reference genome. However, my BAM files were aligned using a version of the reference genome without 'chr' prefixes in the contig names (e.g., 1, 2, ..., instead of chr1, chr2, ...).

I understand that the GATK-provided PON (1000g_pon.hg38.vcf.gz) and germline resource (af-only-gnomad.hg38.vcf.gz) files contain 'chr'-prefixed contigs, which causes a mismatch during Mutect2 execution.

Could you please let me know:

If non-‘chr’-prefixed versions of these files are available for download?

If not, is there an official recommendation for converting the contig names in the VCF files or in the BAM/reference to ensure consistency?

Thank you in advance for your help.

Best regards,

pon hg38 vcf mutect2 gatk
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by dpgpfkdkeldi • dpgpfkdkeldi

1 answer

If not, is there an official recommendation for converting the contig names in the VCF files or in the BAM/reference to ensure consistency?

not "official" but you should replace the chromosome names with bcftools annotate --rename-chrs and set the dictionary (lines starting with ##contig= ) in the header using bcftools reheader .

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written by Pierre Lindenbaum Pierre Lindenbaum

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