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Complex_2ormoreindels_framerestoring_RTG.ucsccoding.vcf
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Complex_2ormoreindels_framerestoring_RTG.ucsccoding.vcf
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##fileformat=VCFv4.1
##fileDate=20131031
##source=RTG Core Core vPOST-3.2 build 73b28fc (2013-10-24)
##CL=population -o /results/3/len/mpr/cohort-mpr-fix/population_1 -t /data/1/1000g_v37_phase2/sdf --region 1 -I /results/3/len/mpr/family_all-sam-files-mpr.txt --pedigree-connectivity=dense --pedigree /results/3/family_caller/19_indv.ped
##RUN-ID=8e941764-77d4-4ebb-a7c7-d4d701e847be
##TEMPLATE-SDF-ID=f1765b39-de93-481a-925d-282fe62ec8a6
##reference=/data/1/1000g_v37_phase2/sdf
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##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##FILTER=<ID=OC,Description="Coverage threshold exceeded">
##FILTER=<ID=RC,Description="RTG variant is a complex region">
##FILTER=<ID=RX,Description="RTG variant contained within hypercomplex region">
##FILTER=<ID=RCEQUIV,Description="RTG variant is equivalent to the previous variant">
##FILTER=<ID=OTHER,Description="Variant is invalid for unknown reasons">
##FILTER=<ID=PHI,Description="This variant has a phasing incompatibility">
##FILTER=<ID=PHO,Description="This variant was outside the regions of known phasing">
##FILTER=<ID=PHR,Description="This variant should be ignored as it has been replaced by a variant with a repair for phasing incompatibility">
##FILTER=<ID=PME,Description="This variant should be ignored as the genotype ploidy of some of the samples did not match the expected ploidy">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Combined read depth for variant over all samples">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##SAMPLE=<ID=NA12878,Sex=FEMALE>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
5 139931629 . C GTCG 42511.3 PASS . GT 1|1
6 90577707 . GACATCTTTGCCCAGACATGGA ACAT 18414 PASS . GT 1|0
11 76751541 . CT C 25673.7 PASS . GT 1|1
11 76751585 . TGGCCCTTCGGCGTGCAGCT GGCCCTTCGGCGTGCAGC 67273.9 PASS . GT 1|1
14 29261308 . AA CAAAC 11968.1 PASS . GT 1|0
14 74060508 . C A 28953.1 PASS . GT 1|0
14 74060512 . AGCTTA TCAAAG 28953.1 PASS . GT 1|0
19 2341059 . GT AC 42699.6 PASS . GT 1|1
19 2341094 . CTCCCTGGAG A 27053.8 PASS . GT 1|0