calc_ase

Calculate per variant read counts

Arguments

input/output options:
    -b|--bam        BAM file containing RNA-seq reads
    -f|--vcf        Genotype VCF for sample
    -o|--output     Name of output ASE file; defaults to lorals_out/ase.tsv

ase options:
    -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

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

Input Formats

BAM file

Standard BAM 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