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From: Aisha Y. <ais...@ym...> - 2018-06-29 04:06:08
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Hi, I ran vcftools on my example file using following command: vcftools --gzvcf test.vcf.gz --remove-indels --min-alleles 2 --max-alleles 2 --recode --out test.bi.vcf It generates log file as well as output file. According to log info file doesn't contain any sites while I get out put file having "4633769" no. of sites. Can you please figure out why log file and output file are not reconciling? Thanks! Log file is like this: VCFtools - v0.1.13 (C) Adam Auton and Anthony Marcketta 2009Parameters as interpreted: --gzvcf test.vcf.gz --max-alleles 2 --min-alleles 2 --out test.bi.vcf --recode --remove-indelsUsing zlib version: 1.2.3 Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files. After filtering, kept 1 out of 1 Individuals Outputting VCF file... After filtering, kept 4633769 out of a possible -1613936332 Sites File does not contain any sites Run Time = 40248.00 seconds |