Conversion of Omni25_genotypes_1525_samples_v2.b37.PASS.ALL.sites.vcf to hg38 fails

[mmok...@gmail.com]

Hi,

  I wanted to lift over the csg.sph.umich.edu/kang/verifyBamID/download/Omni25_genotypes_1525_samples_v2.b37.PASS.ALL.sites.vcf.gz file to hg38 but picard's LiftoverVcf dies with:

Exception in thread "main" java.lang.IllegalStateException: Key AC found in VariantContext field INFO at 1:534247 but this key isn't defined in the VCFHeader.  We require all VCFs to have complete VCF headers by default.

  The trick by adding VALIDATION_STRINGENCY=LENIENT to the commandline does not help in this case so I will probably need to to manually fix the VCF header. However, you may want to fix the file on the website and even better would you also provide version based on hg38 coordinates.

--- Omni25_genotypes_1525_samples_v2.b37.PASS.ALL.sites.vcf.old        2017-05-25 22:12:49.000000000 +0200
+++ Omni25_genotypes_1525_samples_v2.b37.PASS.ALL.sites.vcf    2017-05-25 22:23:27.000000000 +0200
@@ -13,6 +13,8 @@
 ##INFO=<ID=CR,Number=.,Type=Float,Description="SNP Callrate">
 ##INFO=<ID=GentrainScore,Number=.,Type=Float,Description="Gentrain Score">
 ##INFO=<ID=HW,Number=.,Type=Float,Description="Hardy-Weinberg Equilibrium">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
 ##reference=human_g1k_v37.fasta
 ##source=infiniumFinalReportConverterV1.0
 #CHROM POS     ID      REF     ALT     QUAL    FILTER  INFO

BTW, before running picard's Liftover I also had to convert chromosome naming from [1, 2, ..., MT] to [chr1, chr2, chrM] with:

sed -e 's/^1/chr1/' Omni25_genotypes_1525_samples_v2.b37.PASS.ALL.sites.vcf | sed -e 's/^2/chr2/' | sed -e 's/^3/chr3/' | sed -e 's/^4/chr4/' | sed -e 's/^5/chr5/' | sed -e 's/^6/chr6/' | sed -e 's/^7/chr7/' | sed -e 's/^8/chr8/' | sed -e 's/^9/chr9/' | sed -e 's/^X/chrX/' | sed -e 's/^Y/chrY/' | sed -e 's/^MT/chrM/' > Omni25_genotypes_1525_samples_v2.b37.PASS.ALL.sites.new-style.vcf

Hope this helps,

Martin