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