Hi, I want to run GetPileupSummaries (GATK 4.1.8.1) on BAM file aligned to hg38. Could you recommend me which vcf reference file should I use?
For the co-cleaning step with GATK RealignerTargetCreator as "known_indels.vcf" file I used reference from NCBI repository: https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/
I wanted to use it for GetPileupSummaries as well, but I got the error: "A USER ERROR has occurred: Bad input: Population vcf does not have an allele frequency (AF) info field in its header."
I checked and indeed this dbSNP common vcf file doesn't have the AF field - I found the information that allele frequencies are reported now in the CAF tag. (info from here: https://www.ncbi.nlm.nih.gov/variation/docs/oldglossary_dbSNP1_vcf/)
Should I modify the reference to obtain AF from CAF field?
Generally, for GetPileupSummaries it is suggested to use gnomAD as a reference, so I downloaded reference file from here: https://gnomad.broadinstitute.org/downloads/
But I got the error: "A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found contigs with the same name but different lengths."
What would you suggest me to do? I will be grateful for any help, thank you!
