Difference between revisions of "SEQLinkage Commands in Exercise"
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__NOTITLE__ | __NOTITLE__ | ||
| − | ==SEQLinkage Commands in Exercise | + | ==SEQLinkage Commands in Exercise== |
<pre>seqlink -h | <pre>seqlink -h | ||
awk '{if ($0~/^#/) {print} else {{maf=substr($8,12)}; if (maf<=0.01) {print}}}' hearing_with_high_freq.vcf >hearing.vcf | awk '{if ($0~/^#/) {print} else {{maf=substr($8,12)}; if (maf<=0.01) {print}}}' hearing_with_high_freq.vcf >hearing.vcf | ||
Latest revision as of 15:38, 7 June 2018
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
