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TargetsManager: BED not sorted at position #47

Closed rashidma closed 5 years ago

rashidma commented 5 years ago

I am working with tvc 5.10-11 (a3f44efe59-4492b243) - Torrent Variant Caller to call variants from exome data. The command is as follows- tvc --num-threads 10 -r $REF --input-bam $input/SRR5682283_sorted.bam --target-file $input/AmpliseqExome.20141120_effective_regions.nooverlap.bed --output-dir $outdir

But, i always get the following similar error -

TargetsManager: BED not sorted at position 0 replaced :6:193238-193809 with :0:68928-69134 terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::substr

Any help will be highly appreciated. I sorted the BED file with bedtools sort. But, no luck. Thanks

uma-ramasubramanian commented 5 years ago

Thank you for reporting the issue. Please follow the below support channels based on your region for further support: ngs-amsupport@thermofisher.com (Americas) ngs-eusupport@thermofisher.com (EMEA) ngs-gcsupport@thermofisher.com (Greater China) ngs-sasiasupport@thermofisher.com (South Asia) jptech@thermofisher.com (Japan) APAC customers, please contact your local sales representative, Field Service Engineer or Field Bioinformatics Specialist .