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=== Samples information === * HAPMAPPT01: [http://ccr.coriell.org/sections/Search/Panel_Detail.aspx?PgId=202&Ref=HAPMAPPT01] {| {{table}} | align="center" style="background:#f0f0f0;"|'''Catalog ID''' | align="center" style="background:#f0f0f0;"|'''Sex''' | align="center" style="background:#f0f0f0;"|'''Family''' | align="center" style="background:#f0f0f0;"|'''Relationship''' |- | GM11995||Female||1362||maternal grandmother |- | GM11993||Female||1362||paternal grandmother |- | GM10861||Female||1362||mother |- | GM11992||Male||1362||paternal grandfather |- | GM11994||Male||1362||maternal grandfather |- | GM10860||Male||1362||father |- | GM12813||Female||1454||paternal grandmother |- | GM12802||Female||1454||mother |- | GM12815||Female||1454||maternal grandmother |- | GM12812||Male||1454||paternal grandfather |- | GM12814||Male||1454||maternal grandfather |- | GM12801||Male||1454||father |}<br> * Retrieved the genotypes of HAPMAP samples from, http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2008-07_phaseIII/ http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/2008-07_phaseIII/hapmap_format/forward/ *Note: I didn't download from the latest version since it didn't include some samples I am analyzing. * GO.wget.sh: [[Media:GO.wget.txt]] * Concatenate genotypes in from every chromosome into the same file: HAPMAP.genotypes_CEU_phase3.1_nr.b36_fwd.txt * Print out only the column containing the genotypes of samples in family 1362 and 1454: to list the number of column: head -1 HAPMAP.genotypes_CEU_phase3.1_nr.b36_fwd.txt | sed s'/\ /\n/g' > tmp awk '{print $1" "$2" "$3" "$4" "$5" "$76" "$75" "$78" "$77" "$74" "$79" "$138" "$142" "$137" "$140" "$139" "$141;}' HAPMAP.genotypes_CEU_phase3.1_nr.b36_fwd.txt > HAPMAP1362-1454.genotypes_CEU_phase3.1.txt 1,402,288 sites * Since the HAPMAP genotype files were built in hg18, I used Dinh's script to lift over snp's RS values to hg19 positions. * liftoverRSvalues.pl: [[Media:liftoverRSvalues.txt]] ./liftoverRSvalues.pl /GenomeDB/HsGenome/snp134_snv.txt <HAPMAP1362-1454.genotypes_CEU_phase3.1.txt>HAPMAP1362-1454.genotypes_phase3.1.hg19snp134 ** Note: after using lift over, I found the numbers of SNPs before and after lift over were different by increasing more than 30,000 sites. I would figure out what is the cause. wc -l HAPMAP_1363-1454_genotypes.txt --> 1,402,289 SNPs wc -l HAPMAP_1363-1454_genotypes_hg19.snp134 --> 1,438,444 SNPs 1438444 - 1,402,288 = 36,156 SNPs * Dinh suggested to remove the sites in column3 containing 6_apd_hap1 or *_random etc.. awk '{if ($3 !~ /_/) print $0;}' HAPMAP1362-1454.genotypes_phase3.1.hg19snp134 > HAPMAP1362-1454.genotypes_phase3.1.hg19snp134.txt * I got total 1,400,104 sites
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