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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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| The columns are CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, Genotype fields denoted by the sample name. | | The columns are CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, Genotype fields denoted by the sample name. |
| | | |
− | 22 36662041 . AATAATT A 756 PASS AC=2;AN=114;AF=0.0175439;GC=55,2,0;GN=57; | + | 22 36662041 . AATAATT A 756 PASS AC=2;AN=114;AF=0.0175439;GC=55,2,0;GN=57; |
− | GF=0.964912,0.0350877,0;NS=57;
| + | GF=0.964912,0.0350877,0;NS=57; |
− | HWEAF=0.019571;HWEGF=0.961242,0.038376,0.000383024;
| + | HWEAF=0.019571;HWEGF=0.961242,0.038376,0.000383024; |
− | MLEAF=0.0196187;MLEGF=0.960762,0.0392374,2.11537e-15;
| + | MLEAF=0.0196187;MLEGF=0.960762,0.0392374,2.11537e-15; |
− | HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1;
| + | HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1; |
− | FIC=-0.00372601;AB=0.384578
| + | FIC=-0.00372601;AB=0.384578 |
− | GT:PL:DP:AD:GQ 0/0:0,6,145:3:2,0,1:7 0/0:0,12,192:4:4,0,0:12
| + | GT:PL:DP:AD:GQ 0/0:0,6,145:3:2,0,1:7 0/0:0,12,192:4:4,0,0:12 |
| | | |
| Here is a description of the record's fields. | | Here is a description of the record's fields. |
| | | |
− | 22 : chromosome | + | 22 : chromosome |
− | 36662041 : genome position | + | 36662041 : genome position |
− | . : this is the ID field that is left blank. | + | . : this is the ID field that is left blank. |
− | AATAATT : the reference sequence that is replaced by the alternative sequence below. | + | AATAATT : the reference sequence that is replaced by the alternative sequence below. |
− | A : so this is basically a deletion of GT | + | A : so this is basically a deletion of ATAATT. |
− | 756 : QUAL field denoting validity of this variant, higher the better. | + | 756 : QUAL field denoting validity of this variant, higher the better. |
− | PASS : a passed variant. | + | PASS : a passed variant. |
− | INFO : fields containing information about the variant. | + | AC=2... : fields containing information about the variant. |
− | FORMAT : format field labels for the genotype columns. | + | GT:PL:DP:AD:GQ : format field labels for the genotype columns. |
− | 0/0:0,6,145:3:2,0,1:7 : genotype information. | + | 0/0:0,6,145:3:2,0,1:7 : genotype information. |
| | | |
| You can obtain the same output by using the following command | | You can obtain the same output by using the following command |
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| GF=0.96,0.04,0 : genotype frequencies based on GC | | GF=0.96,0.04,0 : genotype frequencies based on GC |
| NS=57 : no. of samples | | NS=57 : no. of samples |
− | HWEAF=0.020 : genotype likelihood based estimation of the allele frequency assuming Hardy Weinberg equilibrium | + | HWEAF=0.020 : genotype likelihood based estimation of the allele frequency assuming Hardy Weinberg equilibrium |
| 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]] |