Process a bunch of GWAS data with rsIDs to a BED file

gwas_data.sh

#for i in GIANT*.txt; do LC_ALL=c sort -k1,1 $i > `basename $i .txt`.sort.bed; done;

export LC_ALL=c
parallel "join -1 4 -2 1 -t $'\t' snp144.sort.bed  {} > {.}.joined.bed" ::: GIANT*sort.bed
parallel "cat {} | awk '{print \$2,\"\t\",\$3,\"\t\",\$4,\"\t\",\$1,\"\t\",\$8}' > {.}.final.bed" ::: *joined.bed
parallel "sort -k1,1 -k2,2n {} > {.}.final.sorted.bed" ::: *.final.bed
parallel "bgzip {}; tabix {}.gz" ::: *.final.sorted.bed

#for i in {1..22};do tabix GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.sort.bed.gz chr$i > GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.chr$i.bed; bgzip GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.chr$i.bed; tabix GIANT_BMI_Speliotes2010_publicrelease_HapMapCeuFreq.chr$i.bed.gz; done;