also added a COVERAGE_CAP option to Picard collectHsMetrics module (default 1000 > picard default which is 200).
we now use a custom version of anaconda utils anacoreUtilsMergeVCFCallersMobiDL.py script to merge the VCFs.
20200625 - Script: autoDL.sh; sometimes, for an undetermined reason, GATK LeftAlignIndels triggers an error:
java.lang.IllegalArgumentException: the range cannot contain negative indices Then, when this error occurs, as this is not a critical step, the pipeline is launched again in a version panelCapture_noGatkLai.wdl that ignores this step.
Until now annovar in achab did not use version number in RefSeq accession numbers (NM). This is corrected using the pragma 'refgeneWithVer' in annovar MobiDL module (hg19 and hg38)
rtg-tools merge was not satisfying and returned a bad number of AD fields when:
- one caller called 2 variants at one site
- the other one called only one variant When merging, rtg retained the 2 variants but with AD of only one variant which triggered an error in bcftools. So rtg-tools was removed and as no satisfying merge method has yet been found, the workflow now outputs 2 files:
- the HaplotypeCaller vcf
- the DeepVariant vcf