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Error while running HaplotypeCaller with reference genome UCSC hg19.fa and NCBI dbSNP.vcf file.

Hello, @bhanuGandham I am trying to run HaplotypeCaller on Exome data, with the UCSC hg19 reference genome. Also, I wanted run against dbsnp.vcf (which I downloaded from the NCBI site) I also created the index file of the dbSNP.vcf file (.idx file was generated). Now when I ran HaplotypeCaller using the command:

./gatk HaplotypeCaller -R /home/vipul/vipul/wes/hg19.fa -I /home/vipul/vipul/wes/IITK-P4-TD/IITK-P4-TD.recal.bam --dbsnp /home/vipul/vipul/wes/dbSNP_ALL_hg19_151_contig_modified.vcf -O variantsP4TDSNP.vcf

I am getting an error:


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]
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, MT]


I am unable to troubleshoot, how to create a right index file of dbSNP.vcf.
I know the fact that UCSC hg19.fa file has "Chr" added to its indexed or fasta file, so is not the case with dbSNP fasta files (I guess).

Your help would be of great help. I am new to this WES analysis. Look forward to your response.


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