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zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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remove.monosnp=TRUE remove all SNPs #45

Open timedreamer opened 6 years ago

timedreamer commented 6 years ago

Hi Xiuwen,

When I run snpgdsIBS on my VCF file, it seems all SNP are removed because of they are recognized as monomorphic SNP. But on my file, they do not look like so. Am I missing something? I attached a few lines of my VCF file here.

Thank you for your time!

Ji

##fileformat=VCFv4.2
##FILTER=<ID=q25,Description="Quality below 25">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FILTER=<ID=q30,Description="Quality below 30">
##source_20180921.1=vcf-merge(r953) intersection_6909.vcf.gz intersection_7025.vcf.gz intersection_7058.vcf.gz intersection_7067.vcf.gz intersection_7111.vcf.gz intersection_7186.vcf.gz intersection_7288.vcf.gz intersection_7347.vcf.gz intersection_7373.vcf.gz intersection_8297.vcf.gz intersection_8387.vcf.gz
##sourceFiles_20180921.1=0:intersection_6909.vcf.gz,1:intersection_7025.vcf.gz,2:intersection_7058.vcf.gz,3:intersection_7067.vcf.gz,4:intersection_7111.vcf.gz,5:intersection_7186.vcf.gz,6:intersection_7288.vcf.gz,7:intersection_7347.vcf.gz,8:intersection_7373.vcf.gz,9:intersection_8297.vcf.gz,10:intersection_8387.vcf.gz
##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  6909    7025    7058    7067    7111    7186    7288    7347    7373    8297    8387
1       73      .       C       A       30.00   PASS    AC=2;AN=2;DP=17;SF=8    GT:DP:GQ        .       .       .       .       .       .       .       .       1|1:17:30       .       .
1       92      .       A       C       28.00   PASS    AC=2;AN=2;DP=4;SF=4     GT:DP:GQ        .       .       .       .       1|1:4:28        .       .       .       .       .       .
1       98      .       T       A       28.00   PASS    AC=2;AN=2;DP=6;SF=9     GT:DP:GQ        .       .       .       .       .       .       .       .       .       1|1:6:28        .
1       110     .       G       T       32.00   PASS    AC=2;AN=2;DP=9;SF=4     GT:DP:GQ        .       .       .       .       1|1:9:32        .       .       .       .       .       .
1       138     .       T       C       32.50   PASS    AC=8;AN=8;DP=30;SF=2,3,5,6      GT:DP:GQ        .       .       1|1:12:32       1|1:4:28        .       1|1:8:38        1|1:6:32        .       .       .       .
1       200     .       T       A       40.00   PASS    AC=2;AN=2;DP=24;SF=4    GT:DP:GQ        .       .       .       .       1|1:24:40       .       .       .       .       .       .
1       214     .       G       A       40.00   PASS    AC=2;AN=2;DP=29;SF=4    GT:DP:GQ        .       .       .       .       1|1:29:40       .       .       .       .       .       .
1       253     .       T       C       40.00   PASS    AC=2;AN=2;DP=24;SF=4    GT:DP:GQ        .       .       .       .       1|1:24:40       .       .       .       .       .       .
1       266     .       G       A       40.00   PASS    AC=2;AN=2;DP=23;SF=9    GT:GQ:DP        .       .       .       .       .       .       .       .       .       1|1:40:23       .
1       346     .       C       T       40.00   PASS    AC=8;AN=8;DP=60;SF=2,3,5,6      GT:DP:GQ        .       .       1|1:22:40       1|1:16:40       .       1|1:10:40       1|1:12:40       .       .       .       .
1       352     .       G       A       38.00   PASS    AC=4;AN=4;DP=24;SF=8,10 GT:GQ:DP        .       .       .       .       .       .       .       .       1|1:40:20       .       1|1:36:4
1       425     .       C       T       39.00   PASS    AC=4;AN=4;DP=26;SF=8,10 GT:DP:GQ        .       .       .       .       .       .       .       .       1|1:19:40       .       1|1:7:38
1       429     .       G       A       40.00   PASS    AC=2;AN=2;DP=33;SF=4    GT:DP:GQ        .       .       .       .       1|1:33:40       .       .       .       .       .       .
1       471     .       T       G       40.00   PASS    AC=4;AN=4;DP=30;SF=8,10 GT:DP:GQ        .       .       .       .       .       .       .       .       1|1:15:40       .       1|1:15:40
1       502     .       T       C       40.00   PASS    AC=10;AN=10;DP=93;SF=2,3,4,5,6  GT:GQ:DP        .       .       1|1:40:17       1|1:40:25       1|1:40:16       1|1:40:14       1|1:40:21       .       .       .       .
1       508     .       T       C       38.75   PASS    AC=16;AN=16;DP=138;SF=2,3,4,5,6,8,9,10  GT:DP:GQ        .       .       1|1:16:40       1|1:26:40       1|1:18:40       1|1:15:40       1|1:23:40       .       1|1:15:40       1|1:17:38       1|1:8:32