SEQLinkage Commands in Exercise

Revision as of 15:32, 7 June 2018 by Zhihuiz (Talk | contribs)

==SEQLinkage Commands in Exercise

seqlink -h
awk '{if ($0~/^#/) {print} else {{maf=substr($8,12)}; if (maf<=0.01) {print}}}' hearing_with_high_freq.vcf >hearing.vcf
bgzip -c hearing.vcf >hearing.vcf.gz 
tabix -p vcf hearing.vcf.gz
seqlink --fam hearing.fam --vcf hearing.vcf.gz --format MERLIN
seqlink --fam hearing.fam --vcf hearing.vcf.gz --format MERLIN --output nocollapsing --bin 1
seqlink --fam hearing.fam --vcf hearing.vcf.gz --format MERLIN --output completecollapsing --bin 0
seqlink --fam hearing.fam --vcf hearing.vcf.gz --freq EXACSASMAF -o linkageanalysis -K 0.002  --moi AR -W 0 -M 1 --run-linkage
Last modified on 7 June 2018, at 15:32