annotate_ase

Annotate an ASE table with warning flags and gene information

Arguments

input/output options:
    -i|--input      Input ASE table
    -b|--bed        Reference BED file
    -f|--vcf        Genotype VCF for sample
    -o|--output     Name of output ASE file; defaults to lorals_out/ase_annotated.tsv

blacklist options:
    --blacklist blacklist.bed           Blacklist BED file; defaults to included file
    --genotype genotype_warning.bed     Genotype warning BED file
    --mapping multi_mapping.bed         BED file with multi-mapping regions;
                                        defaults to included file

ase stats options:
    -c|--coverage       Minimum coverage for a site to be included; defaults to 20
    -n|--binomial-null  For binomial test, the null ref ratio to test against,
                        pass 'auto' to auto-calculate null ref ratio; defaults to 0.5
    -m|--method         Method for calculating biomial null, choose from mean, median,
                        global; defaults to mean
    --other-threshold   Threshold for issuing an other allele warning; defaults to 0.8
    --indel-threshold   Threshold for issuing an indel warning; defaults to 0.2

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

BED files

Standard BED file format: requires at least a four-column BED file

VCF file

Bgzipped VCF file

Output

A tab-separated table with the following columns:

contig

The chromosome or contig of the variant

position

The position of the variant

variantID

The ID given to the variant

refAllele

The reference allele of the variant

altAllele

The alternate alleles, joined by commas, of the variant

refCount

The count of the reference allele for this variant

altCount

The count of the alternate allele for this variant

totalCount

The total expression (ref + alt) count for this variant

refIndelCount

Ref indel count

altIndelCount

alt indel count

otherBases

The count of other alleles for this variant

rawDepth

The total expression (ref + alt + other) count for this variant

GENOTYPE

The genotype for this variant

GENE_ID

A comma-separated list of gene identifiers for this variant

GENOTYPE_WARNING

Was this variant flagged for being in a region prone to genotyping errors? 1 for yes, 0 for no

BLACKLIST

Was this variant flagged for being in a blacklisted region? 1 for yes, 0 for no

MULTI_MAPPING

Was this variant flagged for being in a region prone to multimapping? 1 for yes, 0 for no

OTHER_ALLELE_WARNING

Was this variant flagged for having a high ratio of other alleles? 1 for yes, 0 for no

HIGH_INDEL_WARNING

Was this variant flagged for having a high ratio of indels? 1 for yes, 0 for no

NULL_RATIO

Null reference ratio used for the binomial test

BINOM_P

p-value for the binomial test

BINOM_P_ADJUSTED

FDR-adjusted p-value