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ValidateVariants Error: Input files reference and features have incompatible contigs

whitneytwhitneyt San FranciscoMember
Hello! I'm sorry if I am not using the correct format to ask this in but:

When using gatk ValidateVariants, I receive the error

``` A USER ERROR has occurred: Input files reference and features have incompatible contigs: Found contigs with the same name but different lengths:
contig reference = 1 / 249250621
contig features = 1 / 249218993.
reference 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, MT, GL000207.1, GL000226.1, GL000229.1, GL000231.1, GL000210.1, GL000239.1, GL000235.1, GL000201.1, GL000247.1, GL000245.1, GL000197.1, GL000203.1, GL000246.1, GL000249.1, GL000196.1, GL000248.1, GL000244.1, GL000238.1, GL000202.1, GL000234.1, GL000232.1, GL000206.1, GL000240.1, GL000236.1, GL000241.1, GL000243.1, GL000242.1, GL000230.1, GL000237.1, GL000233.1, GL000204.1, GL000198.1, GL000208.1, GL000191.1, GL000227.1, GL000228.1, GL000214.1, GL000221.1, GL000209.1, GL000218.1, GL000220.1, GL000213.1, GL000211.1, GL000199.1, GL000217.1, GL000216.1, GL000215.1, GL000205.1, GL000219.1, GL000224.1, GL000223.1, GL000195.1, GL000212.1, GL000222.1, GL000200.1, GL000193.1, GL000194.1, GL000225.1, GL000192.1]
features contigs = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] ```

I am using the human_g1k_v37.fasta as my reference, and a merged vcf created by merging grp1.vcf and grp2.vcf, both of which were run through bcftools fixref function aligned to human_g1k_v37.fasta before merging.

I receive the same error (same contig lengths) when trying to use ValidateVariants on grp1.vcf + humann_g1k_v37.fasta before usingn fixref tool.

Do you have any suggestions on how to fix this?

Thanks in advance!

Answers

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