3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchSeqShop: Variant Calling and Filtering for INDELs Practical, December 2014 (view source)
Revision as of 17:09, 17 December 2014
, 17:09, 17 December 2014→Normalization
== 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">
== 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">
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;
HWEAF=0.019571;HWEGF=0.961242,0.038376,0.000383024;
MLEAF=0.0196187;MLEGF=0.960762,0.0392374,2.11537e-15;
HWE_LLR=-0.0222464;HWE_LPVAL=-0.182794;HWE_DF=1;
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
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.
AC=2... : fields containing information about the variant.
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
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=====
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">
</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">
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">
</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">
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]]
