Closed the-x-at closed 4 years ago
Travis CI fails because file rvtests/vcfUtils/Makefile
has a non-existing target createBCF2Index
, which was added in commit 007841885. I am testing the fix with this line commented out. However, I did not want to check it in, as the main author's intentions for including this target are not clear to me.
Fixes a kinship calculation issue with VCF files containing missing data for individuals (#92). Now calling
vcf2kinship
with the input file as mentioned in #92 returns expected results:File
rvtest-online.kinship
containsRunning the same command for the Balding-Nicols method (replacing
--ibs
by--bn
in the command above) gives the following output:which has zeroes for those pairs that involve the individual with the missing variant,
X
, in line with the output of the fixed IBS method. From looking at the source code, neither classBaldingNicolsKinship
nor currently unused classIBSKinshipImpute
appear to have the issue encountered in classIBSKinship
, so the fix should be complete and consistent.