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+-----------------------------+
| |
| Eagle v2.4.1 |
| November 18, 2018 |
| Po-Ru Loh |
| |
+-----------------------------+
Copyright (C) 2015-2018 Harvard University.
Distributed under the GNU GPLv3+ open source license.
Command line options:
../eagle \
--vcfRef=ref.bcf \
--vcfTarget=target.vcf.gz \
--geneticMapFile=../tables/genetic_map_hg19_withX.txt.gz \
--outPrefix=target.phased
Setting number of threads to 1
[W::hts_idx_load2] The index file is older than the data file: ref.bcf.csi
Reference samples: Nref = 169
Target samples: Ntarget = 8
[W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String
SNPs to analyze: M = 430 SNPs in both target and reference
SNPs ignored: 0 SNPs in target but not reference
215 SNPs in reference but not target
0 multi-allelic SNPs in target
Missing rate in target genotypes: 0.00116279
Filling in genetic map coordinates using reference file:
../tables/genetic_map_hg19_withX.txt.gz
Physical distance range: 3595565 base pairs
Genetic distance range: 10.292 cM
Average # SNPs per cM: 42
Number of <=(64-SNP, 1cM) segments: 9
Average # SNPs per segment: 47
Time for reading input: 5.09263 sec
Fraction of heterozygous genotypes: 0.178114
Typical span of default 100-het history length: 13.44 cM
Setting --histFactor=1.00
Auto-selecting number of phasing iterations: setting --pbwtIters to 1
BEGINNING PHASING
PHASING ITER 1 OF 1
Phasing target samples
................................................................................
Time for phasing iter 1: 0.132139
Writing vcf.gz output to target.phased.vcf.gz
[W::vcf_parse] INFO 'AC' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AN' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'DP' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'AFR_AF' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'EX_TARGET' is not defined in the header, assuming Type=String
Time for writing output: 0.0356269
Total elapsed time for analysis = 5.26099 sec
Mean phase confidence of each target individual:
ID PHASE_CONFIDENCE
HG00403 0.953163
HG00404 0.949485
HG00406 0.927005
HG00407 0.950292
HG00419 0.938822
HG00421 0.93367
HG00422 0.952224
HG00428 0.944651
|
