Beagle files using the latest 1000 genomes

Question

[jamespoweraid2]

Hi,

I would like to get the latest beagle files from vcf files from phase 3 of the 1000 genomes data with 2504 unrelated individuals that is here:

http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/, which uses these 1000 Genomes vcf files: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

In particular I am trying to get something like what was available for the previous releases to create the files:

ALL.chr1.phase1_release_v2.20101123.filt.bgl.gz
ALL.chr16.phase1_release_v2.20101123.filt.tabix.gz
ALL.chr1.phase1_release_v2.20101123.filt.markers

Would I need to use the script here with the BEAGLE utilities?

https://data.broadinstitute.org/srlab/BEAGLE/1kG-beagle-release3/READ_ME_beagle_phase1_v3

Thank you so much for any advice about how to get these files in beagle, very very much appreciated...

Answer 1

[Kamil]

Use the BEAGLE tools to change the file format. Here's an example that should get you started:

wget https://faculty.washington.edu/browning/beagle/bref.09Nov15.d2a.jar
wget http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/individual_chromosomes/chr22.1kg.phase3.v5a.bref
java -jar bref.09Nov15.d2a.jar chr22.1kg.phase3.v5a.bref | gzip > chr22.1kg.phase3.v5a.vcf.gz
zcat chr22.1kg.phase3.v5a.vcf.gz | head -n6 | cut -c1-100 | grep -v '^#' | perl -ane 'print join("\t",@F[0..4]),"\t"; $i=0; foreach $G (@F[9..$#F]) { @A = split("\\|", $G, 2); print " " if $i++; print $F[3+$A[0]]," ",$F[3+$A[1]]; }; print "\n"'

Output

22    16050115    rs587755077    G    A    G G G G G G G G G G G G G G G G G G G G G G G G G G G G G G

[jamespoweraid2]

Thank you very much Kamil!

Would this get me the same files as if I ran the script here then?

-- I am trying to get the .filt.bgl.gz, filt.tabix.gz, .filt.markers to be able to run EPIGWAS--

https://data.broadinstitute.org/srlab/BEAGLE/1kG-beagle-release3/READ_ME_beagle_phase1_v3

But using this version of the genome instead?

wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL*
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/phase1*
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/README*

Thanks again!!

[Kamil]

For filtered variants, you might consider taking the files from the BEAGLE website instead of the 1000 Genomes website. The developer of BEAGLE filtered the variants from 1000 Genomes.