Difference between revisions of "SEQLinkage Commands in Exercise"
From Statistical Genetics Courses
(Created page with "__NOTITLE__ <pre> 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 >hea...") |
|||
(2 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
__NOTITLE__ | __NOTITLE__ | ||
− | <pre> | + | ==SEQLinkage Commands in Exercise== |
− | 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 | ||
bgzip -c hearing.vcf >hearing.vcf.gz | bgzip -c hearing.vcf >hearing.vcf.gz |
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