I've been using some SAM (converted to BAM) files and some partial genome assemblies (custom reference sequences) to investigate variants in bulk sequences. GATK's rmdup and Realigner Target Creator had no problem with the files, but when I used them and the output of Realigner Target Creator in Indel Realigner, I got
ERROR MESSAGE: Badly formed genome loc: Parameters to GenomeLocParser are incorrect:Unknown contig . . .
[bam_header_read] EOF marker is absent. The input is probably truncated.
The problem appears to be with the final contig in the reference sequences.
How do I correct this problem?