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when codon has ambiguous nucleotide translate to X
author Jim Johnson <jj@umn.edu>
date Mon, 15 Sep 2014 06:13:47 -0500
parents cdbdac66d6b5
children
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##SnpEffVersion="SnpEff 3.1k (build 2012-12-17), by Pablo Cingolani"
##SnpEffCmd="SnpEff -i vcf -o vcf -upDownStreamLen 0 -no downstream,intergenic,intron,upstream,utr -stats /galaxy/PRODUCTION/database/files/000/246/dataset_246290.dat GRCh37.66 /galaxy/PRODUCTION/database/files/000/246/dataset_246288.dat "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
chr1	46871931	.	GC	G	.	PASS	SAF=0.333333;DP=6;EFF=EXON(MODIFIER|||||FAAH|processed_transcript|CODING|ENST00000489366|2),EXON(MODIFIER|||||FAAH|processed_transcript|CODING|ENST00000493735|6),FRAME_SHIFT(HIGH||-|-281|579|FAAH|protein_coding|CODING|ENST00000243167|7)
chr1	54291558	.	G	GA	.	PASS	SAF=0.333333;DP=12;EFF=EXON(MODIFIER|||||TMEM48|processed_transcript|CODING|ENST00000480952|4),FRAME_SHIFT(HIGH||-/T|-169?|542|TMEM48|protein_coding|CODING|ENST00000540001|5),FRAME_SHIFT(HIGH||-/T|-169?|557|TMEM48|protein_coding|CODING|ENST00000360494|5),FRAME_SHIFT(HIGH||-/T|-169?|674|TMEM48|protein_coding|CODING|ENST00000371429|5),FRAME_SHIFT(HIGH||-/T|-54?|559|TMEM48|protein_coding|CODING|ENST00000234725|4)
chr1	109461327	.	G	A,GA	.	PASS	SAF=0.333333,SAF=0.333333;DP=6;EFF=FRAME_SHIFT(HIGH||-/A|-453?|684|GPSM2|protein_coding|CODING|ENST00000264126|12),FRAME_SHIFT(HIGH||-/A|-453?|684|GPSM2|protein_coding|CODING|ENST00000406462|13),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G452|684|GPSM2|protein_coding|CODING|ENST00000264126|),SYNONYMOUS_CODING(LOW|SILENT|ggG/ggA|G452|684|GPSM2|protein_coding|CODING|ENST00000406462|)