quicKmer-2 index for hs37d5
4 February 2021

Genome reference was downloaded from:
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/

The fasta file was renamed so that there was no text in the fasta header following the record names.

For example:

>1 dna:chromosome chromosome:GRCh37:1:1:249250621:1

was renamed to be

>1.

For the control regions, we excluded known CNVs (not MEI or inversion) from DGV from the following studies:

http://dgv.tcag.ca/dgv/docs/GRCh37_hg19_variants_2020-02-25.txt

1000_Genomes_Consortium_Phase_1
1000_Genomes_Consortium_Phase_3
Conrad_et_al_2009
McCarroll_et_al_2008
Sudmant_et_al_2013

We also removed annotated segmental duplications based on the hg19 track at UCSC.

We further excluded all chromosomes other than 1 - 22. The exclusion file was converted to
an inclusion mask using bedtools.


The index was then made using:

quicKmer2 search -k 30 -t 24 -s 3G -e 2 -d 100 -w 1000 -c ref/include-control.bed ref/hs37d5.fa

and files were gzipped for posting on this web server.