SIFT4G

SIFT4G

SIFT帮助文档SIFT HELP

SIFT官网SIFT HOME

SIFT4G code

Annotate variants with SIFT4G

SIFT 4G Annotator will annotate a variant list (.vcf file) with predictions from a SIFT 4G database.

! VCF file must be sorted by chromosome and position to be annotated properly.

1. If your organism is not listed, you can create your own SIFT prediction database

2. Annotate variants:

To run the SIFT 4G Annotator on Linux or Mac via command line, type the following command into the terminal:

java -jar <Path to SIFT4G_Annotator> -c -i <Path to input vcf file> -d <Path to SIFT4G database directory> -r <Path to your results folder> -t

Note:To run the Annotator via command line "-c" is essential (see the commandline parameters in the table below). If "-t" option is not used SIFT 4G extracts annotator single transcript per variant.

Command line Options:

Option	Description
-c	To run on command line
-i	Path to your input variants file in VCF format
-d	Path to SIFT database directory
-r	Path to your output results folder
-t	To extract annotations for multiple transcripts (Optional)

3. SIFT 4G Output

CHROM	POSITION	REF_ALLELE	ALT_ALLELE	TRANSCRIPT_ID	GENE_ID	GENE_NAME	REGION	VARIANT_TYPE	REF_AA	ALT_AA	AA_POS	SIFT_SCORE	SIFT_MEDIAN	NUM_SEQs	dbSNP	PREDICTION
1	881918	G	A	ENST00000327044	ENSG00000188976	NOC2L	CDS	NONSYNONYMOUS	S	L	556	0.095	2.54	44	rs35471880	TOLERATED
1	900505	G	C	ENST00000338591	ENSG00000187961	KLHL17	CDS	SYNONYMOUS	V	V	621	1	2.62	79	rs28705211	TOLERATED
1	900717	CTTAT	C	ENST00000338591	ENSG00000187961	KLHL17	UTR_3	FRAMESHIFT	DELETION	NA	NA	NA	NA	NA	NA	novel