Pairwise diffs
--pgen-diff <.pgen/.bed filename> <.pvar/.bim> <.psam/.fam>
['include-missing'] ['zs'] ['dosage' | 'dosage='<tolerance>]
['cols='<column set descriptor>]
--pgen-diff <.pgen + .pvar + .psam prefix> ['vzs'] ['include-missing'] ['zs']
['dosage' | 'dosage='<tolerance>] ['cols='<col set descriptor>]
--pgen-diff compares overlapping samples and variants between two filesets (after applying the usual sample and variant filters), and reports unphased genotype/dosage differences to plink2.pdiff.
- If chrX or chrY is present, sex must be defined and consistent. Nonmales are not included in the comparison on chrY.
- Variants are only compared if their IDs and positions match. An error is reported if any such match is not unique.
- The 'vzs' modifier works as with --pfile.
- By default, comparisons are based on genotype hardcalls. Use the 'dosage' modifier to compare dosages instead; you can combine this with a tolerance in [0, 0.5).
- By default, if one genotype is missing and the other isn't, that doesn't count as a difference; this can be changed with the 'include-missing' modifier.
- Refer to the file format entry for output details and optional columns.
--sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]
['include-missing'] [{pairwise | counts-only}] ['zs']
['fname-id-delim='<c>] ['cols='<column set descriptor>]
['counts-cols='<column set descriptor>]
{base= | ids=}<sample ID> <other sample ID(s)...>
--sample-diff ['id-delim='<char>] ['dosage' | 'dosage='<tolerance>]
['include-missing'] [{pairwise | counts-only}] ['zs']
['fname-id-delim='<c>] ['cols='<column set descriptor>]
['counts-cols='<column set descriptor>]
file=<ID-pair file>
(alias: --sdiff)
--sample-diff reports discordances and discordance-counts between pairs of samples. If chrX or chrY is present, sex must be defined and consistent.
- There are three ways to specify which sample pairs to compare.
- To compare a single baseline sample against some others, start the (space-delimited) sample ID list with 'base='.
- To perform an all-vs.-all comparison between the samples you name, start it with 'ids=' instead.
- To compare sample pairs listed in a file (one pair per line), use 'file='.
Note that 'base='/'ids='/'file=' must be positioned after all modifiers.
- Sample IDs are interpreted as if they were in a VCF header line, with 'id-delim=' having the usual effect.
- By default, comparisons are based on hardcalls. Use 'dosage' to compare dosages instead; you can combine this with a tolerance in [0, 0.5).
- By default, if one genotype is missing and the other isn't, that doesn't count as a difference; this can be changed with 'include-missing'.
- By default, a single main report is written to plink2[.<base ID>].sdiff[.zst], and a discordance-count summary is written to plink2.sdiff.summary.
- To write separate pairwise plink2.<ID1>.<ID2>.sdiff[.zst] report files for each compared ID pair, add the 'pairwise' modifier.
- To omit the main report, add the 'counts-only' modifier. (Note that, if you're only interested in nonmissing autosomal biallelic hardcalls, --make-king-table provides a more efficient way to compute just counts.)
- By default, if an output filename has a multipart sample ID, the parts will be delimited by '_'; use 'fname-id-delim=' to change it.
- Refer to the file format entries for other output details and optional columns.
Linkage disequilibrium >>
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