Hi, I'm trying to run the IonTorrent variant caller standalone command line tool with the following command:
./tvc_vcp -r ../hg19.fa -o ~/scratch/p7/wbmet/ -b ../AmpliSeqExome.20141113.designed.bed -i ~/scratch/p7/856om_sorted.bam -n ~/scratch/p7/856wb_sorted.bam
note: tvc_vcp is a symlink to torrent_variant_valler.py
But get this error:
TargetsManager: BED not sorted at position 123252 replaced OR4F21_83939.1.14936:8:116072-116287 with PLCXD1_192345.128:7:200829-201012
TargetsManager: Loaded targets file ../AmpliSeqExome.20141113.designed.bed TargetsManager: 293903 target(s) (168513 after merging) TargetsManager: Targets required sorting
ERROR: Could not open BAM index file(s) :
BamMultiReader::LocatingIndexes: error while locating index files:
BamReader::LocateIndex: could not locate index: BamRandomAccessController::OpenIndex: could not load index data from file: /gpfs/scratch1/3/swist3/p7/856om_sorted.bam.bai BamStandardIndex::CheckMagicNumber: invalid BAI magic number BamReader::LocateIndex: could not locate index: BamRandomAccessController::OpenIndex: could not load index data from file: /gpfs/scratch1/3/swist3/p7/856wb_sorted.bam.bai BamStandardIndex::CheckMagicNumber: invalid BAI magic number
(I apologize for any formatting mistakes) What's confusing is the BED file was taken from Ampliseq.com and should work fine with TorrentVariantCaller. The bed file is sorted by chrStart, why would this "Targets required sorting" prompt come up?
The more important error are the "invalid BAI magic number". I sorted and indexed the bams with samtools....I haven't yet been able to find anything on BAI magic numbers. Do you have any advice?