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 ?
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 ?
Comment