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RealignerTargetCreator error - difference between dbSNP and reference
I'm re-aligning some bam files using RealignerTargetCreator.
I downloaded the hg38 dbSNP file and hg38 reference genome. however, the dbSNP file contains the canonical chromosomes [1,2...X,Y,MT] while the reference (and my bam file) contain also the random chromosomes.
here's where I get the error:
MESSAGE: Input files and reference have incompatible contigs: No overlapping contigs found.
142_hg38.vcf 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]
reference contigs = [chr1, chr1_GL383518v1_alt, chr1_GL383519v1_alt, chr1_GL383520v2_alt ... [etc etc etc.....] ... chrX_KI270881v1_alt, chrX_KI270913v1_alt, chrY, chrY_KI270740v1_random, chrM]
so...I would like to keep the random chromosomes in the reference/bam file, so how can I have this run without tossing an error?
or is this not possible and I need to keep ONLY the chrs in the dbSNP file?