Output to Bed Issues

[albeele1]

running Harmonizer-first time after using it on test data a couple of times

Command line:
java -jar GenotypeHarmonizer.jar --input Shukakaa --inputType PLINK_Bed --update-id --output binaryPlinkShukakaa --outputType Plink_BED --ref vdata --variants 500 --min-ld 0.1 –mafAlign 0.1 --keep –debug

Output is fine until:

Error writing output data: Error reading BED file, found data in padding bits of variant: rs6675994

WHat does this mean and more importantly how do I fix it?

[PatrickDeelen]

Its looks like your BED file is corrupt. You can try to use plink to read your file and recreate it again. But if it is indeed corrupt this might still result in erroneous data.

[albeele1]

I regenerated the Bed file from the Ped file in PLINK. That seemed to fix the issue. Thanks!