Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/93bb9da26a7cf7d0fbe7208bec9baa/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/09/93bb9da26a7cf7d0fbe7208bec9baa/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/253e9038d239bba3c7ead946c79ea2/custom_Sig_18_tumor_normal.manta.somatic_sv.vcf.gz
==> STAGING COMPLETE (4 inputs)


VCFtools - 0.1.16
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
	--gzvcf custom_Sig_18_tumor_normal.manta.somatic_sv.vcf.gz
	--FILTER-summary
	--out custom_Sig_18_tumor_normal.manta.somatic_sv

Using zlib version: 1.2.11
Warning: Expected at least 2 parts in INFO entry: ID=JUNCTION_SOMATICSCORE,Number=1,Type=Integer,Description="If the SV junctino is part of an EVENT (ie. a multi-adjacency variant), this field provides the SOMATICSCORE value for the adjacency in question only">
Warning: Expected at least 2 parts in FORMAT entry: ID=SR,Number=.,Type=Integer,Description="Split reads for the ref and alt alleles in the order listed, for reads where P(allele|read)>0.999">
Warning: Expected at least 2 parts in FORMAT entry: ID=MaxMQ0Frac,Description="For a small variant (<1000 bases) in the normal sample, the fraction of reads with MAPQ0 around either breakend exceeds 0.4">
After filtering, kept 2 out of 2 Individuals
Outputting Filter Summary (for bi-allelic loci only)
After filtering, kept 0 out of a possible 0 Sites
File does not contain any sites
Run Time = 0.00 seconds
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