Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/3471ea2fcb099908972881cc3f0eff/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/3471ea2fcb099908972881cc3f0eff/.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/dc/101a362418abb51764f109c578a6e0/custom_Sig_18_tumor_normal.manta.diploid_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.diploid_sv.vcf.gz
	--out custom_Sig_18_tumor_normal.manta.diploid_sv
	--TsTv-by-qual

Using zlib version: 1.2.11
Warning: Expected at least 2 parts in INFO entry: ID=JUNCTION_QUAL,Number=1,Type=Integer,Description="If the SV junction is part of an EVENT (ie. a multi-adjacency variant), this field provides the QUAL value for the adjacency in question only">
Warning: Expected at least 2 parts in FORMAT entry: ID=FT,Number=1,Type=String,Description="Sample filter, 'PASS' indicates that all filters have passed for this sample">
Warning: Expected at least 2 parts in FORMAT entry: ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
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=Ploidy,Description="For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation">
Warning: Expected at least 2 parts in FORMAT entry: ID=MaxMQ0Frac,Description="For a small variant (<1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4">
Warning: Expected at least 2 parts in FORMAT entry: ID=NoPairSupport,Description="For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample.">
After filtering, kept 1 out of 1 Individuals
Outputting Ts/Tv By Quality
After filtering, kept 6 out of a possible 6 Sites
Run Time = 0.00 seconds
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