Alexander Mikheyev

Dear Pasi, Thank you so much -- everything works now. Sasha

Dear Pasi, Once agian, thank you for the help and the feedbak. So how do I code the (non-genotyped) grandparents that are common to the three parents. I tried giving them their own family number (gives 504 error), or duplicated once for each family (Error 512 Too many parents in a family). Yours, Sasha

Dear Pasi, Thank you so much for the rapid and informative responses! OK, this is embarassing... I though I could bootstrap my earlier example into a complete design, but I was wrong. I actually have a half-sib design where three F1 siblings (2 females and 1 male) mated to each other to give rise to two F2 families. I can't seem to figure out how to code this correctly. Do I include the grand-parental IDs in the pedigree file? What family ID does the male get, since he's part of both families? The...

Dear Pasi, Yes, this works, thank you! Sasha

Dear Pasi, Thank you for the suggestion. I changed the IDs, but still get the same error. I am attaching thea subset of the VCF and the whole pedigree file, in case these give you some more insight. Yours, Sasha

Hi, I am trying to run ParentCall2 using a FreeBayes vcf as input, but get the dreaded 504 error: java.lang.NullPointerException at DataParser.getParentsAndGrandParents(DataParser.java:153) at DataParser.getParentsAndGrandParents(DataParser.java:107) at DataParser.getNextLine(DataParser.java:622) at DataParser.getNextLine(DataParser.java:544) at ParentCall2.callParents(ParentCall2.java:109) at ParentCall2.main(ParentCall2.java:913) Error 504 Error: Unable to load input file or errors in the file...