SMuRFv3.0.1

March 2024

• Fixed datatype conversion bug: Error in set(meta_data, NULL, ind[i], as.numeric(meta_data[[ind[i]]])) :
  'list' object cannot be coerced to type 'double'; Calls: smurf -> parsevcf_allfeaturesall -> set

SMuRFv3.0.0

Jan 2024

• Compatible with bcbio-nextgen 1.2.9 pipeline.
• Capable of processing FFPE WGS samples with tens of millions of mutations called by at least 1 caller.
• Added header to the parse file [minor].

SMuRFv2.0.12

4th Nov 2022

• T_altDepth_Strelka2 calculation update

SMuRFv2.0.11

SMuRFv2.0.10 [redacted]

• royxgen documentation issues

SMuRFv2.0.10

14th April 2022

• Duplicate check for snv and indel parse [minor]

SMuRFv2.0.9

16th April 2021

• CDS annotation additional filter: Filter off indel deletion ranges which may pick up other mutations
• CDS annotation artifacts: Filter 'PASS' and 'MinAF' calls directly after reading in the vcf

SMuRFv2.0.8

5th April 2021
-Updated CDS annotations to detect vcf artifacts, filter to accept 'PASS' and 'MinAF' calls

SMuRFv2.0.7

12th Jan 2021

• Modified column reading for callers without any PASS SNV/Indels (NAs)
• Remove 'roi' redundancy
• Remove vd_SOR warnings for -Inf on NA

SMuRFv2.0.6

18th Nov 2020

• Corrected gr/df column check for callers without any PASS SNV/Indels (NAs)

SMuRFv2.0.5

2nd Nov 2020

• Corrected file detection before annotation. No snv/indel predictions, annotation will be skipped.
• Detect/checking genome build. Use find.build to force change ref genome build according to vcf info.