Test-drive the GATK tools and Best Practices pipelines on Terra
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BQSR non overlapping contigs error
I am trying to run BQSR and I'm getting the non overlapping contigs error that seems to come from mismatched reference and known sites vcf files. My code is below. What I'm trying to figure out is how I can tell which files are matched. I tried the gnomAD exome vcf, which to my understanding is hg19, but apparently not the same format. My reference genome is from UCSC. I have downloaded dbSNP 151 but I expect that will be NCBI format so I'm not sure that will help. Can you offer some guidance on which files match and how to tell?
Also, in terms of documentation, it would be helpful if the tool doc mentioned that the .vcf needs to be indexed.
gatk BaseRecalibrator \
-I $SCRATCH/active/memtest2/SRR112728.marked_duplicates.sorted.bam \
-R $WORK/hg19.fa \
--known-sites $WORK/gnomad.exomes.r2.1.1.sites.vcf.bgz \
Thanks very much,