calc_asts

Calculate transcript counts assigned to each haplotype

Arguments

input/output options:
    -b|--bam        BAM file containing RNA-seq reads
    -i|--input      Input ASE table
    -o|--output     Name of output ASTS file; defaults to lorals_out/asts.tsv

asts options:
    -m|--mode           ASTS mode, choose from length, quant; defaults to length
    -x|--transcripts    BAM file aligned to transcriptome; used when 'mode' is
                        set to 'quant'
    -w|--window         Window around a variant to calculate number of matches;
                        defaults to 5
    -t--threshold       Minimum number of matches in window around the variant;
                        defaults to 8

filter options:
    -c|--coverage           Minimum overall coverage; defaults to 10
    -a|--allelic-coverage   Minimum coverage per allele; defaults to 5
    -q|--mapq mapping       Minimum mapping quality; defaults to 10
    --filter                For annotated ASE tables, filter based on warnings provided.
                            Choose one or more from bl (blacklisted), gt (genotype),
                            mm (multimapping), other, or indel; pass '--filter' with no
                            extra arguments for all filters

utility options:
    -v|--verbosity  Verbosity level, choose from debug, info, warning, error, critical;
                    defaults to info

Input Formats

ASE table

See the output of calc_ase or annotate_ase

BAM file

Standard BAM file

Output

A tab-separated table with the following columns:

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