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Question: filtering VCF files
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gravatar for Bogdan
11 months ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 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",
                           "AML_out_AF_and_AD_FS_and_SOR_filtered.vcf",
                            filters=FS_SOR_rules)

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 11 months ago by Michael Lawrence9.9k • written 11 months ago by Bogdan480
3
gravatar for Michael Lawrence
11 months ago by
United States
Michael Lawrence9.9k wrote:

Maybe your expression could be something like:

fs & sor | !isSNV(x)

 

ADD COMMENTlink written 11 months ago by Michael Lawrence9.9k

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

ADD REPLYlink written 11 months ago by Bogdan480
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