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Shicheng-Guo / rbiotools

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tabix, awk, sort to handle conflict header setting #13

Open Shicheng-Guo opened 3 years ago

Shicheng-Guo commented 3 years ago

tabix, awk, sort to handle conflict header setting

echo -e '#chromosome\tposition\tref\talt\tchromosome-position-ref-alt\tbeta\tse\tpvalue\tmedian_tpm\tmolecular_trait_object_id\tmolecular_trait_id\tvariant maf\ttype\tac\tan\tr2\tgene_id' >xxx.gz.jnj
zcat xxx.gz | awk 'NR>1{print $0|"sort --parallel=50 -k2,2 -k3,3n"}'|awk '{print $2,$3,$4,$5,$2"-"$3"-"$4"-"$5,$10,$11,$9,$18,$16,$1,$6,$8,$12,$13,$14,$15,$17}' OFS="\t" >> xxx.gz.jnj
rm xxx.gz.jnj.gz
bgzip xxx.gz.jnj
tabix -f -p vcf xxx.gz.jnj.gz
tabix -h xxx.gz.jnj.gz 1:13550-14671