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

Parameters as interpreted:
	--gzvcf HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.vcf.gz
	--out HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv
	--TsTv-by-qual

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 Ts/Tv By Quality
After filtering, kept 2 out of a possible 2 Sites
Run Time = 0.00 seconds
ls: *.vcf: No such file or directory
ls: *.bcf: No such file or directory
ls: *.frq: No such file or directory
ls: *.frq.count: No such file or directory
ls: *.idepth: No such file or directory
ls: *.ldepth: No such file or directory
ls: *.ldepth.mean: No such file or directory
ls: *.gdepth: No such file or directory
ls: *.hap.ld: No such file or directory
ls: *.geno.ld: No such file or directory
ls: *.geno.chisq: No such file or directory
ls: *.list.hap.ld: No such file or directory
ls: *.list.geno.ld: No such file or directory
ls: *.interchrom.hap.ld: No such file or directory
ls: *.interchrom.geno.ld: No such file or directory
ls: *.TsTv: No such file or directory
ls: *.TsTv.summary: No such file or directory
ls: *.TsTv.count: No such file or directory
ls: *.FILTER.summary: No such file or directory
ls: *.sites.pi: No such file or directory
ls: *.windowed.pi: No such file or directory
ls: *.weir.fst: No such file or directory
ls: *.het: No such file or directory
ls: *.hwe: No such file or directory
ls: *.Tajima.D: No such file or directory
ls: *.ifreqburden: No such file or directory
ls: *.LROH: No such file or directory
ls: *.relatedness: No such file or directory
ls: *.relatedness2: No such file or directory
ls: *.lqual: No such file or directory
ls: *.imiss: No such file or directory
ls: *.lmiss: No such file or directory
ls: *.snpden: No such file or directory
ls: *.kept.sites: No such file or directory
ls: *.removed.sites: No such file or directory
ls: *.singletons: No such file or directory
ls: *.indel.hist: No such file or directory
ls: *.hapcount: No such file or directory
ls: *.mendel: No such file or directory
ls: *.FORMAT: No such file or directory
ls: *.INFO: No such file or directory
ls: *.012: No such file or directory
ls: *.012.indv: No such file or directory
ls: *.012.pos: No such file or directory
ls: *.impute.hap: No such file or directory
ls: *.impute.hap.legend: No such file or directory
ls: *.impute.hap.indv: No such file or directory
ls: *.ldhat.sites: No such file or directory
ls: *.ldhat.locs: No such file or directory
ls: *.BEAGLE.GL: No such file or directory
ls: *.BEAGLE.PL: No such file or directory
ls: *.ped: No such file or directory
ls: *.map: No such file or directory
ls: *.tped: No such file or directory
ls: *.tfam: No such file or directory
ls: *.diff.sites_in_files: No such file or directory
ls: *.diff.indv_in_files: No such file or directory
ls: *.diff.sites: No such file or directory
ls: *.diff.indv: No such file or directory
ls: *.diff.discordance.matrix: No such file or directory
ls: *.diff.switch: No such file or directory