Variant annotation tutorial - Revision history

Gross016 at 10:25, 22 January 2016

2016-01-22T10:25:37Z

← Older revision		Revision as of 12:25, 22 January 2016
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	=== Extracting variants using BEDtools ===		=== Extracting variants using BEDtools ===

	You will very often want to extract variants based on interval files, e.g. a certain region on a chromosome. This can be easily ~~achieve~~ using the tabix command described above. However, sometimes you may want to extract a substantial number of intervals. You could use tabix in a loop, either as a shell-script or in a scripting language like Perl or Python. However, BedTools provides many utilities for manipulating interval data, such as BED, VCF, or GTF/GFF formats.		You will very often want to extract variants based on interval files, e.g. a certain region on a chromosome. This can be easily achieved by using the tabix command described above. However, sometimes you may want to extract a substantial number of intervals. You could use tabix in a loop, either as a shell-script or in a scripting language like Perl or Python. However, BedTools provides many utilities for manipulating interval data, such as BED, VCF, or GTF/GFF formats.

	Say you are interested in the variants in all the genes lying between coordinates 1,000,000 and 2,000,000 on chromosome 18. The annotation of genes can be found in a GTF file. The GTF file for the UMD3.1 genome build can be found at Ensembl and downloaded using the command line.		Say you are interested in the variants in all the genes lying between coordinates 1,000,000 and 2,000,000 on chromosome 18. The annotation of genes can be found in a GTF file. The GTF file for the UMD3.1 genome build can be found at Ensembl and downloaded using the command line.

Megen002 at 16:46, 12 March 2015

2015-03-12T16:46:22Z

← Older revision		Revision as of 18:46, 12 March 2015
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	<source lang='bash'>		<source lang='bash'>
	SESSIONDIR=/home/formacion/COMUNES/IAMZ/data/CIHEAM/sessions/variant_annotation		SESSIONDIR=/home/formacion/COMUNES/IAMZ/data/CIHEAM/sessions/variant_annotation
			</source>
			And make sure python3 can be found:
			<source lang='bash'>
			alias python3='/home/formacion/COMUNES/IAMZ/soft/python-3.4.2/bin/python3.4'
	</source>		</source>

Megen002: /* Slicing and dicing of VCF files */

2015-03-12T11:40:33Z

Slicing and dicing of VCF files

← Older revision		Revision as of 13:40, 12 March 2015
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	<source lang='bash'>		<source lang='bash'>
	tabix -h /~~home/formacion/COMUNES/IAMZ/data/CIHEAM/MULTISAMPLE_VCF/all.fb~~.vcf.gz 18 \| bgzip >BT18.vcf.gz		tabix -h $SESSIONDIR/allbt.vcf.gz 18 \| bgzip >BT18.vcf.gz
	tabix -p vcf BT18.vcf.gz		tabix -p vcf BT18.vcf.gz
	</source>		</source>

Megen002: /* Slicing and dicing of VCF files */

2015-03-12T11:30:42Z

Slicing and dicing of VCF files

← Older revision		Revision as of 13:30, 12 March 2015
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	<source lang='bash'>		<source lang='bash'>
	tabix -h /home/formacion/COMUNES/IAMZ/data/CIHEAM/MULTISAMPLE_VCF/~~allbt~~.vcf.gz 18 \| bgzip >BT18.vcf.gz		tabix -h /home/formacion/COMUNES/IAMZ/data/CIHEAM/MULTISAMPLE_VCF/all.fb.vcf.gz 18 \| bgzip >BT18.vcf.gz
	tabix -p vcf BT18.vcf.gz		tabix -p vcf BT18.vcf.gz
	</source>		</source>

Megen002: /* A further look at the VEP output */

2015-03-08T17:09:15Z

A further look at the VEP output

← Older revision		Revision as of 19:09, 8 March 2015
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	'technology.ILLUMINA': '1', 'QA': '70', 'EPPR': '3.13803', 'SAP': '3.0103', 'RPPR': '11.1853', 'PQR': '0',		'technology.ILLUMINA': '1', 'QA': '70', 'EPPR': '3.13803', 'SAP': '3.0103', 'RPPR': '11.1853', 'PQR': '0',
	'NS': '8', 'CIGAR': '1X', 'TYPE': 'snp', 'AF': '0.125', 'ABP': '0', 'LEN': '1', 'AC': '0', 'MEANALT': '1',		'NS': '8', 'CIGAR': '1X', 'TYPE': 'snp', 'AF': '0.125', 'ABP': '0', 'LEN': '1', 'AC': '0', 'MEANALT': '1',
	'PAIRED': '1', 'AO': '2', 'AN': '16', 'MQM': '60', 'RUN': '1', 'PRO': '0', 'RPP': '3.0103'}, 'GT:DP:RO:QR:AO:QA:GL',		'PAIRED': '1', 'AO': '2', 'AN': '16', 'MQM': '60', 'RUN': '1', 'PRO': '0', 'RPP': '3.0103'}, ['GT:DP:RO:QR:AO:QA:GL',[
	'0/0:7:7:263:0:0:0,-1.92588,-10', '0/0:7:7:238:0:0:0,-1.92376,-10', '0/0:9:7:266:2:70:-3.90732,0,-10',		'0/0:7:7:263:0:0:0,-1.92588,-10', '0/0:7:7:238:0:0:0,-1.92376,-10', '0/0:9:7:266:2:70:-3.90732,0,-10',
	'0/0:10:10:362:0:0:0,-2.73805,-10', '0/0:10:10:345:0:0:0,-2.73789,-10', '0/0:8:8:287:0:0:0,-2.19662,-10',		'0/0:10:10:362:0:0:0,-2.73805,-10', '0/0:10:10:345:0:0:0,-2.73789,-10', '0/0:8:8:287:0:0:0,-2.19662,-10',
	'0/0:5:5:178:0:0:0,-1.38409,-10', '0/0:14:14:482:0:0:0,-3.82032,-10']		'0/0:5:5:178:0:0:0,-1.38409,-10', '0/0:14:14:482:0:0:0,-3.82032,-10']]]
	</source>		</source>

Megen002: /* If time permits: a human example */

2015-03-08T13:52:16Z

If time permits: a human example

← Older revision		Revision as of 15:52, 8 March 2015
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	<source lang='bash'>		<source lang='bash'>
	java -Xmx4G -jar $snpEff -dataDir $SESSIONDIR/snpEff/data -v GRCh38.78 $SESSIONDIR/common_and_clinical.vcf >common_clinical_snpEff.vcf		java -Xmx4G -jar $snpEff -dataDir $SESSIONDIR/snpEff/data -v GRCh38.78 \
			$SESSIONDIR/common_and_clinical.vcf >common_clinical_snpEff.vcf
	</source>		</source>

Megen002: /* snpEff */

2015-03-08T13:51:39Z

snpEff

← Older revision		Revision as of 15:51, 8 March 2015
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	BT18_rsnumbers.vcf.gz # requires an input file, can be gzipped		BT18_rsnumbers.vcf.gz # requires an input file, can be gzipped
	>testresult_snpEff_Bt.txt # results go to STDOUT and are captured in a file by '>'		>testresult_snpEff_Bt.txt # results go to STDOUT and are captured in a file by '>'


	Study the outcome. Try to filter out 'intergenic' SNPs and other things that are perhaps a bit less relevant (use your skills in 'grep-ping', etc.). What are some of the differences in how the variants are annotated, compared to VEP?		Study the outcome. Try to filter out 'intergenic' SNPs and other things that are perhaps a bit less relevant (use your skills in 'grep-ping', etc.). What are some of the differences in how the variants are annotated, compared to VEP?

Megen002: /* snpEff */

2015-03-08T13:49:36Z

snpEff

← Older revision		Revision as of 15:49, 8 March 2015
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	<source lang='bash'>		<source lang='bash'>
	echo $~~SNP~~		echo $snpEff
	/home/formacion/COMUNES/IAMZ/soft/snpEff/snpEff.jar		/home/formacion/COMUNES/IAMZ/soft/snpEff/snpEff.jar
	</source>		</source>

Megen002: /* Variant Effect Predictor */

2015-03-08T13:46:05Z

Variant Effect Predictor

← Older revision		Revision as of 15:46, 8 March 2015
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	Have a look inside the output file and study its content. Why are there no SNPs in this list that are intergenic?		Have a look inside the output file and study its content. Why are there no SNPs in this list that are intergenic?

	The VEP output you generated before has many advantages, one of which is that it is nicely tabular and easy to parse. In fact a demonstration of that will be covered in the 'Provean' practical. For some purposes, however, it might be more convenient to have the annotations directly in the VCF. Furthermore, you may want annotations for each and every SNP, even if e.g. they are intergenic. You could for instance do the following, omitting the '--no_intergenic and --coding_only flags, and in stead adding the --vcf flag:		The VEP output you generated before has many advantages, one of which is that it is nicely tabular and easy to parse. In fact a demonstration of that will be covered in the 'Provean' practical. For some purposes, however, it might be more convenient to have the annotations directly in the VCF. Furthermore, you may want annotations for each and every SNP, even if e.g. they are intergenic. You could for instance do the following, omitting the '--no_intergenic' and '--coding_only' flags, and in stead adding the '--vcf' flag:
	<source lang='bash'>		<source lang='bash'>
	gunzip -c BT18_rsnumbers.vcf.gz \| \		gunzip -c BT18_rsnumbers.vcf.gz \| \

Megen002: /* Variant Effect Predictor */

2015-03-08T13:44:37Z

Variant Effect Predictor

← Older revision		Revision as of 15:44, 8 March 2015
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	=== Variant Effect Predictor ===		=== Variant Effect Predictor ===

	Various tools exist to make more precise annotations than what you can achieve using Bedtools and a GTF. Among them are Variant Effect Predictor (VEP), snpEff, and Annovar. For the current practical we will use former two.		Various tools exist to make more precise annotations than what you can achieve using Bedtools and a GTF. Among them are Variant Effect Predictor (VEP), snpEff, and Annovar. For the current practical we will use the former two.

	VEP can be found here:		VEP can be found here: