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| == Setup in person at the SeqShop Workshop == | | == Setup in person at the SeqShop Workshop == |
| ''This section is specifically for the SeqShop Workshop computers.'' | | ''This section is specifically for the SeqShop Workshop computers.'' |
− | <div class="mw-collapsible" style="width:600px"> | + | <div class="mw-collapsible mw-collapsed" style="width:600px"> |
| ''If you are not running during the SeqShop Workshop, please skip this section.'' | | ''If you are not running during the SeqShop Workshop, please skip this section.'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| == Setup when running on your own outside of the SeqShop Workshop == | | == Setup when running on your own outside of the SeqShop Workshop == |
| ''This section is specifically for running on your own outside of the SeqShop Workshop.'' | | ''This section is specifically for running on your own outside of the SeqShop Workshop.'' |
− | <div class="mw-collapsible mw-collapsed" style="width:600px"> | + | <div class="mw-collapsible" style="width:600px"> |
| ''If you are running during the SeqShop Workshop, please skip this section.'' | | ''If you are running during the SeqShop Workshop, please skip this section.'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| HWEGF=0.96,0.04,0.00 : genotype frequency derived from HWEAF | | HWEGF=0.96,0.04,0.00 : genotype frequency derived from HWEAF |
| HWE_LPVAL=-0.18 : log p value of HWE test | | HWE_LPVAL=-0.18 : log p value of HWE test |
− | FIC=-0.003 : genotype likelihood based inbreeding coefficient | + | FIC=-0.003 : genotype likelihood based inbreeding coefficient, ranges -1 to 1. <0 denotes excess of heterozygotes and >0 means excess of homozygotes assuming HWE. |
− | AB=0.38 : genotype likelihood based allele balance | + | AB=0.38 : genotype likelihood based allele balance, ranges 0 to 1 with 0.5 for balance, >0.5 meaning reference bias and <0.5 denoting alternate allele bias. |
| | | |
| =====GENOTYPE field===== | | =====GENOTYPE field===== |
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| It is usually useful to examine the call sets against known data sets for the passed variants. | | It is usually useful to examine the call sets against known data sets for the passed variants. |
− | <div class="mw-collapsible" style="width:500px"> | + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| ''Command to use at SeqShop Workshop:'' | | ''Command to use at SeqShop Workshop:'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| </div> | | </div> |
| </div> | | </div> |
− | <div class="mw-collapsible mw-collapsed" style="width:500px"> | + | <div class="mw-collapsible" style="width:500px"> |
| ''Commands outside of SeqShop Workshop:'' | | ''Commands outside of SeqShop Workshop:'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity. | | We perform the same analysis for the failed variants again, the relatively low overlap with known data sets imply a reasonable tradeoff in sensitivity and specificity. |
| | | |
− | <div class="mw-collapsible" style="width:500px"> | + | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
| ''Command to use at SeqShop Workshop:'' | | ''Command to use at SeqShop Workshop:'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| </div> | | </div> |
| </div> | | </div> |
− | <div class="mw-collapsible mw-collapsed" style="width:500px"> | + | <div class="mw-collapsible" style="width:500px"> |
| ''Command outside of SeqShop Workshop:'' | | ''Command outside of SeqShop Workshop:'' |
| <div class="mw-collapsible-content"> | | <div class="mw-collapsible-content"> |
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| | | |
| UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO. | | UMICH's algorithm for normalization has been adopted by Petr Danecek in bcftools and is also used in GKNO. |
| + | |
| + | |
| + | == Return to Workshop Wiki Page == |
| + | Return to main workshop wiki page: [[SeqShop: December 2014]] |