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GATK4: CollectAlleleCount output & Model ModelSegments
I am trying to run the CNV discovery pipeline and I have noticed that the header of sample.allelicCounts.tsv (produced by CollectAlleleCount) gives problems when used to rum ModelSegments.
Indeed, ModelSegments gives me this error:
"A USER ERROR has occurred: Bad input: Bad header in file. Not all mandatory columns are present. Missing: POSITION, REF_COUNT, REF_NUCLEOTIDE, ALT_NUCLEOTIDE, ALT_COUNT"
And I think it's because of the CollectAlleleCount tsv header format:
"CONTIG POSITION REF_COUNT ALT_COUNT REF_NUCLEOTIDE ALT_NUCLEOTIDE"
Is there any specific option to modify the column order? Can I directly parse the file?