Question: Hi,

I am trying to run GATK's `BaseRecalibrator` on a BAM file created with the [hg19 reference sequence downloaded from UCSC website][1].

For the `--known-sites` option I would like to use either a [gnomAD .vcf file][2] or a [dbSNP .vcf][3], downloaded from their respective websites.

The analysis works if I use the `00-common_all.vcf` file from dbSNP; however this file was created on hg38, and I cannot find the hg19 equivalent on their website.

The analysis does not work, on the other hand, when providing any `gnomAD.vcf` file; the chromosome nomenclature on the reference does not correspond to the one in the `.vcf` file, and the following error occurs:

A USER ERROR has occurred: Input files reference and features have incompatible contigs: No overlapping contigs found.
reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr20, chrY, chr19, chr22, chr21, chr6_ssto_hap7, chr6_mcf_hap5, chr6_cox_hap2, chr6_mann_hap4, chr6_apd_hap1, chr6_qbl_hap6, chr6_dbb_hap3, chr17_ctg5_hap1, chr4_ctg9_hap1, chr1_gl000192_random, chrUn_gl000225, chr4_gl000194_random, chr4_gl000193_random, chr9_gl000200_random, chrUn_gl000222, chrUn_gl000212, chr7_gl000195_random, chrUn_gl000223, chrUn_gl000224, chrUn_gl000219, chr17_gl000205_random, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chr9_gl000199_random, chrUn_gl000211, chrUn_gl000213, chrUn_gl000220, chrUn_gl000218, chr19_gl000209_random, chrUn_gl000221, chrUn_gl000214, chrUn_gl000228, chrUn_gl000227, chr1_gl000191_random, chr19_gl000208_random, chr9_gl000198_random, chr17_gl000204_random, chrUn_gl000233, chrUn_gl000237, chrUn_gl000230, chrUn_gl000242, chrUn_gl000243, chrUn_gl000241, chrUn_gl000236, chrUn_gl000240, chr17_gl000206_random, chrUn_gl000232, chrUn_gl000234, chr11_gl000202_random, chrUn_gl000238, chrUn_gl000244, chrUn_gl000248, chr8_gl000196_random, chrUn_gl000249, chrUn_gl000246, chr17_gl000203_random, chr8_gl000197_random, chrUn_gl000245, chrUn_gl000247, chr9_gl000201_random, chrUn_gl000235, chrUn_gl000239, chr21_gl000210_random, chrUn_gl000231, chrUn_gl000229, chrM, chrUn_gl000226, chr18_gl000207_random, chr1_jh806574_fix, chr1_gl949741_fix, chr1_jh636053_fix, chr1_jh636052_fix, chr1_gl383518_alt, chr1_gl383519_alt, chr1_gl383520_alt, chr1_jh806573_fix, chr1_jh636054_fix, chr1_jh806575_fix, chr1_gl383516_fix, chr1_gl383517_fix, chr2_gl383521_alt, chr2_kb663603_fix, chr2_gl877871_fix, chr2_gl582966_alt, chr2_gl383522_alt, chr2_gl877870_fix, chr3_jh636055_alt, chr3_jh159132_fix, chr3_gl383523_fix, chr3_ke332495_fix, chr3_gl383524_fix, chr3_jh159131_fix, chr3_gl383525_fix, chr3_gl383526_alt, chr4_ke332496_fix, chr4_gl383528_alt, chr4_gl383529_alt, chr4_gl582967_fix, chr4_gl383527_alt, chr4_gl877872_fix, chr5_gl383532_alt, chr5_gl949742_alt, chr5_gl339449_alt, chr5_gl383530_alt, chr5_jh159133_fix, chr5_ke332497_fix, chr5_gl383531_alt, chr6_jh806576_fix, chr6_jh636057_fix, chr6_gl383533_alt, chr6_kb663604_fix, chr6_jh636056_fix, chr6_ke332498_fix, chr6_kb021644_alt, chr7_gl582970_fix, chr7_gl582969_fix, chr7_ke332499_fix, chr7_jh159134_fix, chr7_gl582972_fix, chr7_gl582968_fix, chr7_jh636058_fix, chr7_gl383534_alt, chr7_gl582971_fix, chr8_gl949743_fix, chr8_ke332500_fix, chr8_jh159135_fix, chr8_gl383535_fix, chr8_gl383536_fix, chr9_gl383539_alt, chr9_jh636059_fix, chr9_gl383540_alt, chr9_gl383541_alt, chr9_gl383542_alt, chr9_kb663605_fix, chr9_jh806579_fix, chr9_gl339450_fix, chr9_jh806577_fix, chr9_jh806578_fix, chr9_gl383537_fix, chr9_gl383538_fix, chr10_gl877873_fix, chr10_jh636060_fix, chr10_gl383543_fix, chr10_gl383545_alt, chr10_gl383546_alt, chr10_jh591181_fix, chr10_kb663606_fix, chr10_jh591183_fix, chr10_ke332501_fix, chr10_jh591182_fix, chr10_gl383544_fix, chr10_jh806580_fix, chr11_jh591184_fix, chr11_jh591185_fix, chr11_gl383547_alt, chr11_gl582973_fix, chr11_jh159136_alt, chr11_jh159137_alt, chr11_gl949744_fix, chr11_jh806581_fix, chr11_jh159143_fix, chr11_jh159141_fix, chr11_jh159139_fix, chr11_jh159142_fix, chr11_jh159140_fix, chr11_jh720443_fix, chr11_jh159138_fix, chr12_gl582974_fix, chr12_gl877875_alt, chr12_jh720444_fix, chr12_gl949745_alt, chr12_gl877876_alt, chr12_gl383549_alt, chr12_gl383550_alt, chr12_gl383552_alt, chr12_gl383553_alt, chr12_kb663607_fix, chr12_gl383551_alt, chr12_gl383548_fix, chr13_gl582975_fix, chr14_kb021645_fix, chr15_gl383554_alt, chr15_gl383555_alt, chr15_jh720445_fix, chr16_gl383556_alt, chr16_jh720446_fix, chr16_gl383557_alt, chr17_jh806582_fix, chr17_gl383563_alt, chr17_gl383562_fix, chr17_gl383561_fix, chr17_ke332502_fix, chr17_jh159145_fix, chr17_kb021646_fix, chr17_gl383560_fix, chr17_gl383559_fix, chr17_jh159146_alt, chr17_jh159148_alt, chr17_jh159147_alt, chr17_gl383564_alt, chr17_gl582976_fix, chr17_jh720447_fix, chr17_gl383558_fix, chr17_jh159144_fix, chr17_gl383565_alt, chr17_gl383566_alt, chr17_jh591186_fix, chr17_jh636061_fix, chr18_gl383567_alt, chr18_gl383570_alt, chr18_gl383571_alt, chr18_gl383568_alt, chr18_gl383569_alt, chr18_gl383572_alt, chr19_jh159149_fix, chr19_gl582977_fix, chr19_gl383573_alt, chr19_gl383575_alt, chr19_gl383576_alt, chr19_gl383574_alt, chr19_ke332505_fix, chr19_kb021647_fix, chr19_gl949746_alt, chr19_gl949747_alt, chr19_gl949748_alt, chr19_gl949749_alt, chr19_gl949750_alt, chr19_gl949751_alt, chr19_gl949752_alt, chr19_gl949753_alt, chr20_gl383577_alt, chr20_jh720448_fix, chr20_kb663608_fix, chr20_gl582979_fix, chr21_gl383578_alt, chr21_gl383579_alt, chr21_gl383580_alt, chr21_gl383581_alt, chr21_ke332506_fix, chr22_jh806584_fix, chr22_jh806583_fix, chr22_jh806585_fix, chr22_jh720449_fix, chr22_gl383583_alt, chr22_gl383582_alt, chr22_kb663609_alt, chr22_jh806586_fix, chrX_gl877877_fix, chrX_jh720451_fix, chrX_jh720452_fix, chrX_jh806589_fix, chrX_kb021648_fix, chrX_jh806590_fix, chrX_jh806587_fix, chrX_jh806591_fix, chrX_jh806592_fix, chrX_jh720453_fix, chrX_jh720454_fix, chrX_jh806593_fix, chrX_jh806594_fix, chrX_jh806595_fix, chrX_jh720455_fix, chrX_jh806588_fix, chrX_jh806601_fix, chrX_jh806602_fix, chrX_jh806603_fix, chrX_jh806596_fix, chrX_jh806597_fix, chrX_jh806598_fix, chrX_jh806599_fix, chrX_jh806600_fix, chrX_jh159150_fix, chrMT]
features contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y]

Does anyone have any input .vcf file from either database correctly formatted to be used for this purpose on hg19?
How would you proceed?

Thanks a lot for any input.

[1]: https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz
[2]: https://gnomad.broadinstitute.org/downloads
[3]: https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/

Answer: You have a good grasp on the exact problems you're facing. Here are a few options for you to consider:

1. Rename chromosomes in gnomAD using `bcftools annotate --rename-chrs`
2. Get an hg19 dbSNP VCF file - it should be available, just dig deeper. EDIT: Took just a few extra seconds of navigating the link you pasted to get to this directory: https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF/