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

Question

[dpgpfkdkeldi]

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,

Answer 1

[Pierre Lindenbaum]

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 .