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.
Save SNPs
See here.
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 or more 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,
name1is the name of the firstIndividualname2is the name of the secondIndividualcM_thresholdcorresponds to the same named parameter offind_shared_dna(); “.” is replaced by “p” with precision of 2, e.g., “0p75”snp_thresholdcorresponds to the same named parameter offind_shared_dna()genetic_mapcorresponds to the same named parameter offind_shared_dna().
Note
If more than two individuals are compared, all Individual
names will be included in the filenames and plot titles using the same conventions.
Note
Genetic maps do not have recombination rates for the Y chromosome since the Y chromosome does not recombine. Therefore, shared DNA will not be shown on the Y chromosome.
shared_dna_<name1>_<name2>_<cM_threshold>cM_<snp_threshold>snps_GRCh37_<genetic_map>.png
This plot 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.
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).
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.