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docs/output.md

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@@ -763,14 +763,14 @@ When using pileupCaller for genotyping, single-stranded and double-stranded libr
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- `consensus_sequence/multivcfanalyzer/`
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- `data/`
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- `*fullAlignment.fasta.gz`: FASTA file of all positions contained in the VCF files i.e. including ref calls
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- `*snpAlignment.fasta.gz`: FASTA file of only SNP positions including only the calls of the samples.
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- `*snpAlignment.fasta.gz`: FASTA file of only SNP positions including only the calls of the samples.
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- `*snpAlignmentIncludingRefGenome.fasta.gz`: FASTA file of just SNP positions including reference genome calls.
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- `stats/`
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- `*info.txt`: File with information about the run
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- `*snpStatistics.tsv`: File containing basic statistics about the SNP calls of each sample.
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- `*snpTableForSnpEff.tsv`: Input file for SnpEff.
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- `*snpTable.tsv`: SNP table of combined positions taken from each VCF file, in TSV format.
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- `*snpTableWithUncertaintyCalls.tsv`: SNP table of combined positions taken from each VCF file, in TSV format, but with lower case characters indicating uncertain calls
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- `*snpTableWithUncertaintyCalls.tsv`: SNP table of combined positions taken from each VCF file, in TSV format, but with lower case characters indicating uncertain calls
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- `*structureGenotypes_noMissingData-Columns.tsv`: Alternate input file for STRUCTURE.
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- `*structureGenotypes.tsv`: Input file for STRUCTURE.
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