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Vt

57 bytes added, 14:35, 14 February 2016
Profile VNTRs
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#profile indels found in mills.vcf
vt profile_vntrs -g vntr.reference.txt vt.vcf -r hs37d5.fa
#this is a sample output for indel profiling vt profile_vntrs ../20150812_spectrum/vntrs.sites.bcf -g ~/ref/vt/grch37/vntr.reference.txt profile_vntrs v0.5 # square brackets contain the insOptions: input VCF file ../20150812_spectrum/del ratiovntrs. sites.bcf [g] reference data sets list file # for the FS/NFS field, that is the proportion of coding indels that are frame shiftednet/fantasia/home/atks/ref/vt/grch37/vntr.reference. txt  no VNTRs 5660874 no low complexity # The numbers in curved bracket are the counts of frame shift and non frame shift indels respectively2686460 (47. data set46%) No Indels : 46974 [no coding 17911 (0.89]32%) FS/NFS : no redundant 0.26 1312209 (8/23.18%) <br>  dbsnptrf_lobstr (1638516) A-B 30704 [0.92] 3269285 A-B~ 1666185 A&B1 725404 A&B2 723195 B 16270 [0.83]-A~ 710075 B-A 2049488 [1.52] 205246 Precision 34.6% Sensitivity 0.8% <br>trf_repeatseq (1624553) mills A-B 3291652 A-B 43234 [0.88]~ 1650190 A&B1 719032 A&B 3740 [1.00]B2 716838 B-A ~ 203278 [0.98]703948 Precision 8.0%B-A 203767 Sensitivity 1.8% <br> mills.chiptrf_vntrseek (230306) A-B 46847 [0.89] 5384453 A&-B 127 [0.90]~ 271302 B-A &B1 8777 [0.93]5119 Precision A&B2 4973 0.3%B-A~ 92496 Sensitivity 1.4% <br>B-A 132837   affy.exome.chipcodis+ (15) A-B 46911 [0.89] 5660794 A&-B ~ 63 [0.43]79 B-A 33997 [0.47]&B1 1 Precision A&B2 1 0.1%B-A~ 14 Sensitivity B-A 0.2% <br>
# This file contains information on how to process reference data sets.
# filter - filter applied to variants for this particular data set.
# path - path of indexed BCF file.
#dataset type filter path 1000g trf_lobstr TP N_ALLELE==2&&VTYPE==INDEL VNTR /net/fantasia/home/atks/ref/vt/grch37/1000Gtrf.snps_indelslobstr.sites.bcf mills trf_repeatseq TP N_ALLELE==2&&VTYPE==INDEL VNTR /net/fantasia/home/atks/ref/vt/grch37/millstrf.208620indelsrepeatseq.sites.bcf dbsnp trf_vntrseek TP N_ALLELE==2&&VTYPE==INDEL VNTR /net/fantasia/home/atks/ref/vt/grch37/dbsnptrf.13147541variantsvntrseek.sites.bcf GENCODE_V19 cds_annotation . codis+ TP VTYPE==VNTR /net/fantasia/home/atks/ref/vt/grch37/gencodecodis.cdsstrs.bedsites.gzbcf DUST cplx_annotation GENCODE_V19 cds_annotation . /net/fantasia/home/atks/ref/vt/grch37/mdustgencode.v19.cds.bed.gz DUST cplx_annotation .
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