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Error Message running Discovery-Input file is not sorted by start position
During the very last job of 3000+ jobs submitted with the Discovery qscript, the following error occurred running the VariantFiltration tool.
ERROR MESSAGE: Input file is not sorted by start position.
ERROR We saw a record with a start of 1:56000020 after a record with a start of 1:56000025, for input source: /auto/nfs-archive/ifs/noreplica/project/genpro/archive/adsp/GenomeSTRiP/svtoolkit/adsp/run.Pilot37/adsp.del.sites.unfilte
red.vcf which looks like it was generated during the creation of the tribble index.
When the 1000s of discovery vcf files were concatenated, these 2 calls ended up out of the correct order in adsp.del.sites.unfiltered.vcf.
1 56000025 DEL_P0056_1278 1 56000020 DEL_P0057_1
The 56000025 deletion was the last one found in the P0056 vcf file and the 56000020 the first in P0056 vcf file.
Does a sort step need to be added to the discovery qscript or should these type of out of order calls not happen?