test_comparison: Overlapping and compared SNVs

In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

Description

Overlapping and compared variants from "sample1" and "sample2" originating from the example.vcf file included in the inst/extdata directory, for use in unit tests.

Usage

data(test_comparison)

Format

A dataframe with 51 rows and 39 columns:

chr

chromosome

pos

SNV position

DP.sample_1

total variant depth, sample 1

AD1.sample_1

allelic depth, allele 1, sample 1

AD2.sample_1

allelic depth, allele 2, sample 1

A1.sample_1

allele 1, sample 1

A2.sample_1

allele 2, sample 1

warnings.sample_1

warnings from variant calling, sample 1

DP.sample_2

total variant depth, sample 2

AD1.sample_2

allelic depth, allele 1, sample 2

AD2.sample_2

allelic depth, allele 2, sample 2

A1.sample_2

allele 1, sample 2

A2.sample_2

allele 2, sample 2

warnings.sample_2

warnings from variant calling, sample 2

sample_1

name, sample 1

sample_2

name, sample 2

match

status of genotype comparison

rsID

mutation ID

gene

associated gene

ENSGID

ensembl gene ID

ENSTID

ensembl transcript ID

REF

reference allele

ALT

alternative allele

impact

putative variant impact

effect

variant effect

feature

transcript feature

biotype

transcript biotype

seqCAT documentation built on Nov. 8, 2020, 7:36 p.m.