No overlapping contigs problem
Hi! I have a question about overlapping contigs in HaplotypeCaller:
reference contigs = [KJ776791.2]
reads contigs = []
About input: I used the genome reference (KJ776791.2) to assemble the "zikaparental" genome, but, somehow, the script isn't overlapping the contigs properly.
That is the command:
gatk HaplotypeCaller -R ZIKVref/ZikaAsian.reference.fasta -I Zikaparent_bam_bai/zikaparental.bam -O zikaparental.vcf
I checked my input BAM header:
@SQ SN:KJ776791.2 LN:10807.
How is HaplotypeCaller not overlapping the contigs?
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