Question: filtering VCF files
gravatar for Bogdan
21 months ago by
Palo Alto, CA, USA
Bogdan530 wrote:

Dear all, and dear Valerie, and Martin,

please i would need a bit of help to set up a filter on a VCF file that contains, SNV, INDELs and DELETIONs.

I would like to filter the file based on a 2 fields in the INFO column - FS and SOR (related to strandness), however, these 2 fields are only present in SNV fields of vcf, and not in INSERTION or DELETION records.

And if I set up the filter below, it will work, however it excludes from the final output file the records with INSERTION and DELETIONs (it prints only filtered SNVs). 

FS_SOR_filters = function(x) {
                               fs  <- info(x)$FS <= 60
                               sor <- info(x)$SOR <= 4
                               fs & sor & isSNV(x)

FS_SOR_rules <- FilterRules(list(FS_SOR_filters = FS_SOR_filters))

vcf_filtered <- filterVcf( "AML_out_AF_and_AD_filtered.vcf.bgzip", "hg38",

what shall i do in order to be able to keep the INSERTION and DELETION in the output file, although the records do not contain FS and SOR fields ? thank you very much,


-- bogdan


ADD COMMENTlink modified 21 months ago by Michael Lawrence10k • written 21 months ago by Bogdan530
gravatar for Michael Lawrence
21 months ago by
United States
Michael Lawrence10k wrote:

Maybe your expression could be something like:

fs & sor | !isSNV(x)


ADD COMMENTlink written 21 months ago by Michael Lawrence10k

Thank you for suggestions, Mike ! great, it works !

ADD REPLYlink written 21 months ago by Bogdan530
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 233 users visited in the last hour