Hi, I am getting error message "Problem detecting index type" while combining 200 GVCFs generated by HaplotypeCaller (gatk 3.5). Can you suggest how can i identify source of this error or if this is anything known.
Thanks
INFO 12:09:45,366 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:09:45,536 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 12:09:45,536 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 12:09:45,536 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 12:09:45,540 HelpFormatter - Program Args: -R ref.fasta -T CombineGVCFs -V gVCF-f1.list -o gVCF-f1.g.vcf
INFO 12:09:45,545 HelpFormatter - Date/Time: 2016/08/09 12:09:45
INFO 12:09:45,545 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:09:45,546 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:13:56,334 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:13:56,953 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 12:23:14,035 RMDTrackBuilder - Writing Tribble index to disk for file 1A.g.vcf.idx
INFO 12:27:51,742 RMDTrackBuilder - Writing Tribble index to disk for file 11A.g.vcf.idx
INFO 12:29:15,840 RMDTrackBuilder - Writing Tribble index to disk for file 8A.g.vcf.idx
INFO 12:30:32,400 RMDTrackBuilder - Writing Tribble index to disk for file 9A.g.vcf.idx
INFO 12:32:22,639 RMDTrackBuilder - Writing Tribble index to
disk for file 5A.g.vcf.idx
INFO 12:32:27,187 GATKRunReport - Uploaded run statistics report to AWS S3