snpEff & snpSIFT variant filtering

doc.ramses · 11-15-2011, 01:00 AM

Hi,

I want to filter a .vcf file with snpSIFT and have the problem that I can't use the filter expressions described here: http://snpeff.sourceforge.net/SnpSift.html

I figured out that instead of:
cat variants.vcf | java -jar SnpSift.jar " ( QUAL >= 30 )" > filtered.vcf

I have to use:
java -jar SnpSift.jar filter -f variants.vcf " ( QUAL >= 30 )" > filtered.vcf

to get this done. But I dont' have a clue how to target the INFO field, where all the important information like DP, AF or in case of an snpEFF annotated file the EFF is located. When I use a expression like ( DP > 10 ) I get an error No such field 'DP'...

Anyone ?

Danielbenitezr · 03-05-2014, 07:55 AM

I have the same question:
I need to filter my vcf file by allele frequencies in order to keep only those samples that have differences between each other (polymorphic SNVs), not between them and the reference.
If you got the answer, please share it =)

thanks!

jreuther · 10-21-2014, 01:29 PM

Here you go!

cat VCF_file.vcf | java -jar SnpSift.jar filter "(( QUAL >= 30) & (na ID ) & (DP >= 200) & (AO >= 20) & (SAF >= 5) & (SAR >= 5))" | > Output.vcf

you can do similar commands with different portions of the INFO field. The "na ID" field is for me to output the non-SNPs.

If anyone knows how to combine the ("na ID" or "(exists ID & Eur_AF < .02)) fields, I'd appreciate the knowledge. Right now i have to do two different vcf files and cat them.

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11-15-2011, 01:00 AM	#1
doc.ramses Member Location: Planet Earth Join Date: Jan 2011 Posts: 26	snpEff & snpSIFT variant filtering Hi, I want to filter a .vcf file with snpSIFT and have the problem that I can't use the filter expressions described here: http://snpeff.sourceforge.net/SnpSift.html I figured out that instead of: cat variants.vcf \| java -jar SnpSift.jar " ( QUAL >= 30 )" > filtered.vcf I have to use: java -jar SnpSift.jar filter -f variants.vcf " ( QUAL >= 30 )" > filtered.vcf to get this done. But I dont' have a clue how to target the INFO field, where all the important information like DP, AF or in case of an snpEFF annotated file the EFF is located. When I use a expression like ( DP > 10 ) I get an error No such field 'DP'... Anyone ?

03-05-2014, 07:55 AM	#2
Danielbenitezr Junior Member Location: Concepcion, Chile Join Date: Dec 2012 Posts: 9	I have the same question: I need to filter my vcf file by allele frequencies in order to keep only those samples that have differences between each other (polymorphic SNVs), not between them and the reference. If you got the answer, please share it =) thanks!

10-21-2014, 01:29 PM	#3
jreuther Junior Member Location: houston Join Date: Oct 2014 Posts: 2	Here you go! cat VCF_file.vcf \| java -jar SnpSift.jar filter "(( QUAL >= 30) & (na ID ) & (DP >= 200) & (AO >= 20) & (SAF >= 5) & (SAR >= 5))" \| > Output.vcf you can do similar commands with different portions of the INFO field. The "na ID" field is for me to output the non-SNPs. If anyone knows how to combine the ("na ID" or "(exists ID & Eur_AF < .02)) fields, I'd appreciate the knowledge. Right now i have to do two different vcf files and cat them.