VCFtools - 0.1.16 (C) Adam Auton and Anthony Marcketta 2009 Parameters as interpreted: --gzvcf HCC1395_BL.deconflicted_somatic.vcf.gz --FILTER-summary --out HCC1395_BL.deconflicted_somatic Using zlib version: 1.2.11 Warning: Expected at least 2 parts in FORMAT entry: ID=germline,Description="Evidence indicates this site is germline, not somatic"> Warning: Expected at least 2 parts in FORMAT entry: ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> Warning: Expected at least 2 parts in FORMAT entry: ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> Warning: Expected at least 2 parts in INFO entry: ID=AS_FilterStatus,Number=1,Type=String,Description="Filter status for each allele, as assessed by ApplyRecalibration. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles."> Warning: Expected at least 2 parts in INFO entry: ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)"> Warning: Expected at least 2 parts in FORMAT entry: ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2"> Warning: Expected at least 2 parts in FORMAT entry: ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2"> Warning: Expected at least 2 parts in FORMAT entry: ID=TOR,Number=2,Type=Integer,Description="Other reads (weak support or insufficient indel breakpoint overlap) for tiers 1,2"> Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}."> Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}."> Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}."> Warning: Expected at least 2 parts in INFO entry: ID=NT,Number=1,Type=String,Description="Genotype of the normal in all data tiers, as used to classify somatic variants. One of {ref,het,hom,conflict}."> Warning: Expected at least 2 parts in INFO entry: ID=QSI,Number=1,Type=Integer,Description="Quality score for any somatic variant, ie. for the ALT haplotype to be present at a significantly different frequency in the tumor and normal"> Warning: Expected at least 2 parts in FORMAT entry: ID=SUPPRESS_DECONFLICT,Description="Variant in CHIP/germline grey zone with no COSMIC rescue, or ambiguous germline/somatic — suppressed from both outputs"> Warning: Expected at least 2 parts in INFO entry: ID=DECONFLICT_ASSIGNED,Number=1,Type=String,Description="Category assigned by deconfliction: CHIP, GERMLINE, SUPPRESS, or SUSPECT"> Warning: Expected at least 2 parts in INFO entry: ID=DECONFLICT_ASSIGNED,Number=1,Type=String,Description="Category assigned by deconfliction: CHIP, GERMLINE, SUPPRESS, or SUSPECT"> Warning: Expected at least 2 parts in INFO entry: ID=DECONFLICT_ASSIGNED,Number=1,Type=String,Description="Category assigned by deconfliction: CHIP, GERMLINE, SUPPRESS, or SUSPECT"> After filtering, kept 2 out of 2 Individuals Outputting Filter Summary (for bi-allelic loci only) After filtering, kept 187 out of a possible 187 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: *.TsTv.qual: 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