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This article is about how vcftools calculates the snp deletion rate. The editor thinks it is very practical, so share it with you as a reference and follow the editor to have a look.

Vcftools calculates snp deletion rate

There are two parameters in vcftools to calculate the missing rate of snp in the vcf file.

They are:

-- missing-indv generates a file that reports the absence of each sample, with the suffix ".imiss".

-- missing-site generates a file that reports the deletion of each snp locus, with the suffix ".lmarker".

Specific usage:

Vcftools-- vcf snp.vcf. -- missing-site

Running the above command generates an out.lmiss file in the current directory in the following format:

CHR POS N_DATA N_GENOTYPE_FILTERED N_MISS F_MISSchr01 194921 988 0 368 0.37247chr01 384714 988 0 204 0.206478chr01 384719 988 0 202 0.204453chr01 518438 988 0 488 0.493927chr01 518473 988 0 452 0.45749chr01 518579 988 0 418 0.423077chr01 518635 988 0 428 0.433198chr01 680786 988 0 346 0.350202chr01 680834 988 0 412 0.417004

The first two listed as the location of snp, the third as the total number of alleles, the fifth as the total number of deletions, and the last as the deletion rate.

Vcftools-- vcf snp.vcf. -- missing-indv

Running the above command generates an out.imiss file in the current directory in the following format:

INDV N_DATA N_GENOTYPES_FILTERED N_MISS F_MISS

1 8747 0 3632 0.415228

10 8747 0 1264 0.144507

102 8747 0 2016 0.230479

105 8747 0 6322 0.722762

106 8747 0 2365 0.270378

107 8747 0 4376 0.500286

108 8747 0 5682 0.649594

109 8747 0 1877 0.214588

11 8747 0 1039 0.118784

The first is the sample name, the second is the total number of snp, the fourth is the total number of deletions, and the last is the deletion rate.

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