Data Processing

First steps

A list of individuals present in the local ancestry calls downloaded from 1KGP was first compiled.

Sex information for individuals was obtained from the file:

integrated_call_samples_v3.20130502.ALL.panel

available at:

https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/.

We then identified individuals present in the local ancestry data but missing from this panel.

Individuals Not Included in the Panel

The following command identifies individuals present in the ancestry calls but absent from the panel:

awk '
NR==FNR { seen[$1]=1; next }
!($1 in seen) { print $1 }
' integrated_call_samples_v3.20130502.ALL.panel ./ASW/TrioPhased/individuals.txt

Output:

NA19985
NA20322
NA20336
NA20341
NA20344

Identification of Related Individuals

These individuals correspond to related samples, as listed in:

20140625_related_individuals.txt

available at:

https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/.

The following command confirms this:

awk '
NR==FNR { seen[$1]=1; next }
($1 in seen) { print $1 }
' 20140625_related_individuals.txt ./ASW/TrioPhased/individuals.txt

Output:

NA19985
NA20322
NA20336
NA20341
NA20344

Filtering Related Individuals

These individuals are present in the local ancestry calls but are not independent. They should therefore be removed.

To exclude related individuals:

awk '
NR==FNR { seen[$1]=1; next }
!($1 in seen) { print $1 }
' 20140625_related_individuals.txt ./ASW/TrioPhased/individuals.txt

To save the filtered list:

awk '
NR==FNR { seen[$1]=1; next }
!($1 in seen) { print $1 }
' 20140625_related_individuals.txt ./ASW/TrioPhased/individuals.txt \
> ./ASW/TrioPhased/individuals_unrelated.txt

Output Formatting

To format the list of individuals as a CSV string (e.g., for inclusion in a driver file):

awk '
NR==FNR { seen[$1]=1; next }
($1 in seen) { printf "\"%s\"," , $1 }
' 20140625_related_individuals.txt ./ASW/TrioPhased/individuals.txt

Male Individuals

To extract male individuals in the same format:

awk '
NR==FNR { seen[$1]=1; next }
($1 in seen) { printf "\"%s\"," , $1 }
' ./males_ASW.panel ./ASW/TrioPhased/individuals_unrelated.txt