Change history

Changes in v2.2.0:

• HPTEST and LDBIRD have been added to the repository. See their respective pages for documentation.

• QCTOOL: added -[in|ex]cl-ranges, which behave like -[in|ex]cl-range but read ranges from a file.

• Fix compilation issues: 9c01ec9ee1 and a31af45e24.

Changes in v2.0.8:

• Permit GP field without GT field in VCF format, fixing ticket 4d88dff8cc.
• qctool: always get sample identifiers from input file when they are available and no -s option is supplied. In BGEN format, default is now to write sample identifiers whenever possible unless -bgen-omit-sample-identifier-block is specified. Fixes ticket b952a6be.
• inthinnerator: make sure column specified by -rank-column is output as a FLOAT in sqlite output.

Changes in v2.0.7:

• Use (and expect) semicolons not commas to separate VCF variant IDs.
• Solve compilation failure issue on some versions of gcc.

Changes in v2.0.6:

• qctool: Fix bug in info metric computation when there is missing data.
• inthinnerator: output all columns from the input file.

Changes in v2.0.5

• qctool: fix bug when using -flip-to-match-cohort1 and/or strand alignment with multiple sources.
• inthinnerator: use -o not -odb and add -compare-variants-by.
• inthinnerator: (re-)implement nearest gene-finding algorithm.

Changes in v2.0.1:

• fix bug when reading IMPUTE haplotypes format data.

Changes in v2.0 series:

QCTOOL v2 differs in several important ways from the v1 release series. Some important changes in QCTOOL v2 relative to v1 are:

• Support for more file formats: QCTOOL v2 supports a diverse array of common file formats - see the file formats page for more information.
• Support for more features: QCTOOL v2 has a bunch of features not found in v1 - for example it can compute LD metrics, apply strand alignments, annotate variants with information from external sources, and more.
• Removal of on-the-fly filtering options: The options for direct filtering based on summary statistics (-maf, -hwe, -snp-missing-rate, etc.) have been removed. Instead, it's expected you will inspect summary statistics and manually create lists of variants and/or samples for removal, using the -incl- and -excl- options to exclude them in a seperate QCTOOL run as described here and here. (That's often what you want anyway, since it's useful to have a record of what you've removed.)
• Treatment of chromosomes: QCTOOL v1 always converted chromosomes to a two-digit form (01,02, ...) and would treat chromosomes as missing if they were not of specific forms pertinent to human datasets. QCTOOL v2 instead allows arbitrary strings to be used as chromosomes. This change brings QCTOOL into line with other tools, e.g. those that use contig identifiers from a reference genome build. However, this also breaks some workflows that would previously have worked, namely when matching between datasets that have differently encoded chromosome names. A possible workaround is to use the -map-id-data option to replace chromosome identifiers on the fly during analysis.
• Changes to output of summary stats: QCTOOL performs several types of per-variant summary computation, that are specified using options like -snp-stats and the -annotate- options. When outputting results, all output is sent to a single output file that is specified using the -osnp option. This file will automatically inherit columns from each requested computation. Similarly, all per-sample summary computations are output the file specified by -osample.