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I find the exome_summary.csv
to be one of the most useful files because it brings together nearly all the useful information. Here are the fields in that file (see these docs for more information, or the Annovar filter descriptions page here):
Func | exonic, splicing, ncRNA, UTR5, UTR3, intronic, upstream, downstream, intergenic |
Gene | The common gene name |
ExonicFunc | frameshift insertion/deletion/block subst, stopgain, stoploss, nonframeshift ins/del/block stubst., nonsynonymous SNV, synonymous SNV, or Unknown |
AAChange (in gene coordinates) | |
Conserved (i.e. SNP is in a conserved region) | based on the UCSC 46-way conservation model |
SegDup (snp is in a segmental dup. region) | |
ESP5400_ALL | Alternate Allele Frequency in 3510 NHLBI ESP European American Samples |
1000g2010nov_ALL | Alternative Allele Frequency in 1000 genomes pilot project 2012 Feb release (minor allele could be reference or alternative allele). |
dbSNP132 | The id# in dbSNP if it exists |
AVSIFT | The AVSIFT score of how deleterious the variant might be |
LJB_PhyloP | Conservation score provided by dbNSFP which is re-scaled from original phylop score. The new score ranges from 0-1 with larger scores signifying higher conservation. A recommended cutoff threshold is 0.95. If the score > 0.95, the prediction is "conservative". if the score <0.95, the prediction is "non-conservative". |
LJB_PhyloP_Pred | |
LJB_SIFT | SIFT takes a query sequence and uses multiple alignment information to predict tolerated and deleterious substitutions for every position of the query sequence. Positions with normalized probabilities less than 0.05 are predicted to be deleterious, those greater than or equal to 0.05 are predicted to be tolerated. |
LJB_SIFT_Pred | |
LJB_PolyPhen2 | Functional prediction score for non-syn variants from Polyphen2 provided by dbNSFP (higher score represents functionally more deleterious). A score greater than 0.85 corresponds to prediciton of "probably damaging". The prediciton is "possbily damaging" if score is between 0.85 and 0.15, and "benign" if score is below 0.15. |
LJB_PolyPhen2_Pred | |
LJB_LRT | Functional prediction score for non-syn variants from LRT provided by dbNSFP (higher score represents functionally more deleterious. It ranges from 0 to 1. This score needs to be combined with other information prediction. If a threshold has to be picked up under some situation, 0.995 can be used as starting point. |
LJB_LRT_Pred | |
LRT_MutationTaster | Functional prediction score for non-syn variants from Mutation Taster provided by dbNSFP (higher score represents functionally more deleterious). The score ranges from 0 to 1. Similar to LRT, the prediction is not entirely depending on the score alone. But if a threshold has to be picked, 0.5 is the recommended as the starting point. |
LRT_MutationTaster_Pred | |
LJB_GERP++ | higher scores are more deleterious |
Chr | |
Start | |
End | |
Ref | Reference base |
Obs | Observed base-pair or variant |
SNP Quality value | |
filter information | |
DP=raw read depth, VDB= variant distance bias (might be a problem with RNA seq calls), RPB=read position bias (since early/late bp in a read may be worse), AF1=Max-likelihood estimate of the first ALT allele frequency (assuming HWE), HWE=Chi^2 based HWE test P-value based on G3, AC1=Max-likelihood estimate of the first ALT allele count (no HWE assumption), DP4=# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases, MQ=Root-mean-square mapping quality of covering reads, FQ=Phred probability of all samples being the same, PV4=P-values for strand bias, baseQ bias, mapQ bias and tail distance bias | |
GT:PL:GQ for each file! | |
(ALL the VCF info is here!!) | |
GT:PL:GQ for each file! |
Everything after the "LJB_GERP++" field in exome_summary came from the original VCF file, so this file REALLY contains everything you need to go on to functional analysis! This is one of the many reasons I like Annovar.
Scavenger hunts!
Find the gene with two frameshift deletions in NA12878
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DEFB126 (just grep "frameshift" from the exome_summary file) |
Test "genetic drift" vs. "functional selection" - e.g. is the distribution of variants different among non-coding regions, synonymous changes in coding regions, and non-synonymous changes in coding regions?
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Compare the output of these three commands:
Do you notice a pattern? What's the right statistical test to determine whether non-synonymous mutations might be under different selective pressure than intergenic or synonymous mutations from this data? |
Other variant annotators:
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