Output Files

The various output files produced by lineage are detailed below. Output files are saved in the output directory, which is defined at the instantiation of the Lineage object. Generation of output files can usually be enabled or disabled via a save_output argument to the associated method.

Load SNPs

Multiple raw data files can be loaded when an Individual is instantiated. Alternatively, additional files can be loaded after instantiation using load_snps().

When loading multiple raw data files, if there are any discrepancies between the existing data and the new data, those are noted. Specifically, discrepancies in SNP positions and genotypes are output as CSV files. Output of these files is enabled via the save_output=True argument to load_snps().

<name>_discrepant_positions_<num>.csv

Where name is the name of the Individual and num indicates the file count for discrepant positions files.

Column Description
rsid SNP ID
chrom Chromosome of existing SNP
pos Position of existing SNP
genotype Genotype of existing SNP
chrom_added Chromosome of added SNP
pos_added Position of added SNP (discrepant with pos)
genotype_added Genotype of added SNP

A large number of discrepant positions could indicate that the files contain SNPs from different builds / assemblies.

<name>_discrepant_genotypes_<num>.csv

Where name is the name of the Individual and num indicates the file count for discrepant genotypes files.

Column Description
rsid SNP ID
chrom Chromosome of existing SNP
pos Position of existing SNP
genotype Genotype of existing SNP
chrom_added Chromosome of added SNP
pos_added Position of added SNP
genotype_added Genotype of added SNP (discrepant with genotype)

A large number of discrepant genotypes could indicate that the files contain SNPs for different individuals.

Discrepant SNPs

Summaries can be saved of the discrepant SNPs found while loading files.

<name>_discrepant_positions.csv

Where name is the name of the Individual. SNPs with discrepant positions can be saved with save_discrepant_positions().

Column Description
rsid SNP ID
chrom Chromosome of existing SNP
pos Position of existing SNP
genotype Genotype of existing SNP
chrom_added Chromosome of added SNP
pos_added Position of added SNP (discrepant with pos)
genotype_added Genotype of added SNP

<name>_discrepant_genotypes.csv

Where name is the name of the Individual. SNPs with discrepant genotypes can be saved with save_discrepant_genotypes().

Column Description
rsid SNP ID
chrom Chromosome of existing SNP
pos Position of existing SNP
genotype Genotype of existing SNP
chrom_added Chromosome of added SNP
pos_added Position of added SNP
genotype_added Genotype of added SNP (discrepant with genotype)

<name>_discrepant_snps.csv

Where name is the name of the Individual. SNPs with discrepant positions and / or genotypes can be saved with save_discrepant_snps().

Column Description
rsid SNP ID
chrom Chromosome of existing SNP
pos Position of existing SNP
genotype Genotype of existing SNP
chrom_added Chromosome of added SNP
pos_added Position of added SNP (possibly discrepant with pos)
genotype_added Genotype of added SNP (possibly discrepant with genotype)

Save SNPs

The SNPs for an Individual can be saved with save_snps(). One CSV file is output when SNPs are saved.

<name>_lineage_<assembly>.csv

Where name is the name of the Individual and assembly is the assembly of the SNPs being saved.

Column Description
rsid SNP ID
chromosome Chromosome of SNP
position Position of SNP
genotype Genotype of SNP

Find Discordant SNPs

Discordant SNPs between two or three individuals can be identified with find_discordant_snps(). One CSV file is optionally output when save_output=True.

discordant_snps_<name1>_<name2>_GRCh37.csv

Where name1 is the name of the first Individual and name2 is the name of the second Individual.

Column Description
rsid SNP ID
chrom Chromosome of SNP
pos Position of SNP
genotype_<name1> Genotype of first individual
genotype_<name2> Genotype of second individual

discordant_snps_<name1>_<name2>_<name3>_GRCh37.csv

Where name1 is the name of the first Individual, name2 is the name of the second Individual, and name3 is the name of the third Individual.

Column Description
rsid SNP ID
chrom Chromosome of SNP
pos Position of SNP
genotype_<name1> Genotype of first individual
genotype_<name2> Genotype of second individual
genotype_<name3> Genotype of third individual

Find Shared DNA

Shared DNA between two individuals can be identified with find_shared_dna(). One PNG file and up to two CSV files are output when save_output=True.

In the filenames below, name1 is the name of the first Individual and name2 is the name of the second Individual.

Note that shared DNA will not be shown on the Y chromosome since the Y chromosome does not recombine; therefore, genetic maps do not have recombination rates for the Y chromosome.

shared_dna_<name1>_<name2>.png

The plot that illustrates shared DNA (i.e., no shared DNA, shared DNA on one chromosome, and shared DNA on both chromosomes). The centromere for each chromosome is also detailed. Two examples of this plot are shown below.

https://raw.githubusercontent.com/apriha/lineage/master/docs/images/shared_dna_User662_User663.png

In the above plot, note that the two individuals only share DNA on one chromosome. In this plot, the larger regions where “No shared DNA” is indicated are due to SNPs not being available in those regions (i.e., SNPs were not tested in those regions).

https://raw.githubusercontent.com/apriha/lineage/master/docs/images/shared_dna_User4583_User4584.png

In the above plot, the areas where “No shared DNA” is indicated are the regions where SNPs were not tested or where DNA is not shared. The areas where “One chromosome shared” is indicated are regions where the individuals share DNA on one chromosome. The areas where “Two chromosomes shared” is indicated are regions where the individuals share DNA on both chromosomes in the pair (i.e., the individuals inherited the same DNA from their father and mother for those regions). Note that the regions where DNA is shared on both chromosomes is a subset of the regions where one chromosome is shared.

shared_dna_one_chrom_<name1>_<name2>_GRCh37.csv

If DNA is shared on one chromosome, a CSV file details the shared segments of DNA.

Column Description
segment Shared DNA segment number
chrom Chromosome with matching DNA segment
start Start position of matching DNA segment
end End position of matching DNA segment
cMs CentiMorgans of matching DNA segment
snps Number of SNPs in matching DNA segment

shared_dna_two_chroms_<name1>_<name2>_GRCh37.csv

If DNA is shared on two chromosomes, a CSV file details the shared segments of DNA.

Column Description
segment Shared DNA segment number
chrom Pair of chromosomes with matching DNA segment
start Start position of matching DNA segment on each chromosome
end End position of matching DNA segment on each chromosome
cMs CentiMorgans of matching DNA segment on each chromosome
snps Number of SNPs in matching DNA segment on each chromosome

Find Shared Genes

Shared genes (with the same genetic variations) between two individuals can be identified with find_shared_dna(), with the parameter shared_genes=True. In addition to the outputs produced by Find Shared DNA, up to two additional CSV files are output that detail the shared genes when save_output=True.

In the filenames below, name1 is the name of the first Individual and name2 is the name of the second Individual.

shared_genes_one_chrom_<name1>_<name2>_GRCh37.csv

If DNA is shared on one chromosome, this file details the genes shared between the two individuals on at least one chromosome; these genes are located in the shared DNA segments specified in shared_dna_one_chrom_<name1>_<name2>_GRCh37.csv.

Column* Description*
name Name of gene
geneSymbol Gene symbol
chrom Reference sequence chromosome or scaffold
strand + or - for strand
txStart Transcription start position (or end position for minus strand item)
txEnd Transcription end position (or start position for minus strand item)
refseq RefSeq ID
proteinID UniProt display ID, UniProt accession, or RefSeq protein ID
description Description

* UCSC Genome Browser / UCSC Table Browser

shared_genes_two_chroms_<name1>_<name2>_GRCh37.csv

If DNA is shared on both chromosomes in a pair, this file details the genes shared between the two individuals on both chromosomes; these genes are located in the shared DNA segments specified in shared_dna_two_chroms_<name1>_<name2>_GRCh37.csv.

The file has the same columns as shared_genes_one_chrom_<name1>_<name2>_GRCh37.csv.