tests

A repository to share problems under development.

Tests for turboqq & turboman

• turboqq for https://github.com/bpprins/turboqq

• turboman for https://github.com/bpprins/turboman

  > options(width=200)
  > load("turboman_hg19_reference_data.rda")
  > ls()
  [1] "ld_block_breaks_pickrell_hg19_eur" "refgene_gene_coordinates_h19"
  > head(ld_block_breaks_pickrell_hg19_eur)
    chr   start
  1   1   10583
  2   1 1892607
  3   1 3582736
  4   1 4380811
  5   1 5913893
  6   1 7247335
  > head(refgene_gene_coordinates_h19)
        chromosome gene_transcription_start gene_transcription_stop  gene_name gene_transcription_midposition
  1              1                    11873                   14409    DDX11L1                        13141.0
  53009          1                    17368                   17436  MIR6859-1                        17402.0
  55877          1                    17368                   17436  MIR6859-3                        17402.0
  2              1                    14361                   29370     WASH7P                        21865.5
  45554          1                    30365                   30503 MIR1302-10                        30434.0
  45166          1                    30365                   30503  MIR1302-9                        30434.0
  

• Annotation files which be can used to build turboman_hg19_reference_data.rda.

  • glist-hg19 and glist-hg38, https://www.cog-genomics.org/plink/1.9/resources
  • ldetect-data, https://bitbucket.org/nygcresearch/ldetect-data/src/master/

• The IL-12B example,

  • IL.12B.txt.gz was split via split --bytes=45M "IL.12B.txt.gz" "IL.12B.txt-"
  • It could be recoverd via cat IL.12B.txt-* > IL.12B.txt.gz

SNPid generation

A SNPid (chr:pos_a1/a2) often replaces RSid as an unique variant identifier in genetic association studies. A customised implemention for a compressed VCF file based on Bash is as follows,

#!/usr/bin/bash

function snpid2()
{
  gunzip -c ${1} | \
  awk -v use_I_D_as_alleles=0 -v FS="\t" -v OFS="\t" -v out=${2} '
  NR==1,/#CHROM/{print;next}
  {
    if (length($4)>1||length($5)>1) {if (length($4)>length($5)) {a1="I"; a2="D"} else {a1="D"; a2="I"}; $3=$1":"$2"_D/I"} else
       {a1=$4; a2=$5; if (a1<a2) $3=$1":"$2"_"a1"/"a2; else $3=$1":"$2"_"a2"/"a1}
    n=a[$3]++
    if(n>0) {a1=a1 n; a2=a2 n; $3=$1":"$2"_"a1"/"a2 }
    if(use_I_D_as_alleles) {$4=a1; $5=a2}
    if(length($4)>1||length($5)>1) print $1,$2,$3,$4,$5 >> sprintf("%s.txt",out)
    print
  }' | bgzip -f > ${2}-snpid.vcf.gz
  bcftools index -tf ${2}-snpid.vcf.gz
}
rm -f test.txt
snpid2 ERZ127238/HPSI1013i-garx_3.wec.gtarray.HumanCoreExome-12_v1_0.imputed_phased.20150604.genotypes.vcf.gz test

Only definitions for indels are listed. More details are available from the snpid directory.