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The "--f1r2-tar-gz" input is used in FilterMutectCalls (check: https://gatkforums.broadinstitute.org/gatk/discussion/24057/how-to-call-somatic-mutations-using-gatk4-mutect2#latest).
The "---germline-resource" input was already available in gatk 4.1.0.0.

Without this input attribute using the PoN would not be possible.

update changelog

Flag description:
  -M  If set, output only candidate somatic
  -A  Indicate to output all variants at the same position.  By default, only the variant with the highest allele frequency is converted to VCF
  -Q  float The minimum mapping quality.  Defaults to 0 for Illumina sequencing => Using -Q 20 as default
  -d  integer The minimum total depth.  Defaults to 5 => Using -d 8 as default
  -v  integer The minimum variant depth.  Defaults to 3 => Using -v 4 as default
  -f  float The minimum allele frequency.  Defaults to 0.02

Note that "-M" is a soft filter (see https://github.com/AstraZeneca-NGS/VarDictJava/issues/247). This means that there will still be variants with "STATUS=Germline" with a "PASS" filter.

Use compression level 1 in cutadapt.

Add feature type,idattr and additional attributes to htseq-count task.

add allow contain

add task for the chunked-scatter script

Add CNV callers