I have an issue with the Lepmap3 suite and I did not find a solution inthe previous discussions hosted here. If I missed it, sorry for the inconvenience.
Using a vcf file, the ParentCall2 module crashed and give the attached files and error.
vcf files was converted from .bed files with plink 1.9.
I do not understand why the input string "AX-75241406" causes the error when the previous rowes -with the same pattern of input strings- of data work without issue.
I tried to delete the row causing the crash which just made the module stop at the next row.
It seems to be the 5th rows, whatever the string input that causes the bug...
I, now have a second issue, which is error 512 : too many parents.
To be sure, it means that ParentCall need that each family is only composed of one Sire, one Dam and their progenies.
If one Sire has progenies with multiples Dams, each combinaison must be in a different familly. (No half-sibs in the same family.)
Best regards,
Julien.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Yes, you have to have have each full sib family separately with a unique family id. ParentCall2 will detect and utilise half-sib families from common parents. Other modules do not benefit from half-sib information.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Pasi,
I have the same problem. For half-sib families, with one father P1_m1 and two mothers P1_f2, P2_f3, and offspring progy_1,progy_2,...; Should I split this pedigree.txt into two pedigrees ped1 .txt and ped2.txt and execute java ParentCall2 data=ped1.txt vcfFile=test.vcf and java ParentCall2 data=ped2.txt vcfFile=test.vcf respectively? If implemented separately, however, how will ParentCall2 detect and utilize half-sibling families from co-parents?
pedigree.txt
CHROM POS ALL ALL ALL ALL ALL ALL ALL ALL ALL
CHROM POS P1_m1 P1_f2 P2_f3 progy_1 progy_2 progy_3 progy_4 progy_5 progy_6
CHROM POS 0 0 0 P1_m1 P1_m1 P1_m1 P1_m1 P1_m1 P1_m1
CHROM POS 0 0 0 P1_f2 P1_f2 P1_f2 P1_f2 P2_f3 P2_f3
CHROM POS 1 2 2 0 0 0 0 0 0
CHROM POS 0 0 0 0 0 0 0 0 0
You should include both families in one pedigree. The attached pedigree works for me, and ParentCall2 gives the hint "parent P1_m1 occurs 2 times in the pedigree use halfSibs=1 to utilize this information".
Dear Pasi,
Thank you for your response. The ped12.txt file you provided in the attachment seems to be the fourth format mentioned. When executing ParentCall2, should I add the parameter halfSibs=1?
I have another question regarding if both parents of P1_m1 (father), P1_f2, and P2_f3 (two mothers) are known (genotyped or ungenotyped). If I want to provide the parents of both P1_m1 (father), P1_f2, and P2_f3 (two mothers), which would be the progeny's grandfather, should the ped12.txt file be in a similar format as shown in the attachment? Should I also give different family names for each parent of P1_m1?
Best regards,
chinj cheung
Dear Pasi,
Thank you for your response. The ped12.txt file you provided in the attachment seems to be the fourth format mentioned. When executing ParentCall2, should I add the parameter halfSibs=1?
I have another question regarding if both parents of P1_m1 (father), P1_f2, and P2_f3 (two mothers) are known (genotyped or ungenotyped). If I want to provide the parents of both P1_m1 (father), P1_f2, and P2_f3 (two mothers), which would be the progeny's grandfather, should the ped12.txt file be in a similar format as shown in the attachment? Should I also give different family names for each parent of P1_m1?
Best regards,
Yes, you should include halfSibs=1 to ParentCall2 if you have shared parents.
You can add the same grandparent in multiple families, just add the different family ID for each column with the same grandparent. Lep-MAP3 does not use the information of same grandparents, it is handled the same way whether the grandparents are unique to a family or not.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello everyone,
I have an issue with the Lepmap3 suite and I did not find a solution inthe previous discussions hosted here. If I missed it, sorry for the inconvenience.
Using a vcf file, the ParentCall2 module crashed and give the attached files and error.
vcf files was converted from .bed files with plink 1.9.
I do not understand why the input string "AX-75241406" causes the error when the previous rowes -with the same pattern of input strings- of data work without issue.
I tried to delete the row causing the crash which just made the module stop at the next row.
It seems to be the 5th rows, whatever the string input that causes the bug...
Any clues would be very much appreciated.
Thanks,
Julien.
Last edit: Recoquillay Julien 2023-12-07
Dear Julien,
I think you have to provide the vcf file like this:
Where the pedigree file is given via data parameter.
Cheers,
Pasi
Thanks again Pasi, the 504 issue is solved.
I, now have a second issue, which is error 512 : too many parents.
To be sure, it means that ParentCall need that each family is only composed of one Sire, one Dam and their progenies.
If one Sire has progenies with multiples Dams, each combinaison must be in a different familly. (No half-sibs in the same family.)
Best regards,
Julien.
Dear Pasi,
Thanks for the answers. I will try this,as your answer sho me that I misunderstood the Wiki and used :
java ParentCall2 data=test.vcf
Thanks again,
Julien.
Dear Julien,
Yes, you have to have have each full sib family separately with a unique family id. ParentCall2 will detect and utilise half-sib families from common parents. Other modules do not benefit from half-sib information.
Cheers,
Pasi
Dear Pasi,
I have the same problem. For half-sib families, with one father P1_m1 and two mothers P1_f2, P2_f3, and offspring progy_1,progy_2,...; Should I split this pedigree.txt into two pedigrees ped1 .txt and ped2.txt and execute java ParentCall2 data=ped1.txt vcfFile=test.vcf and java ParentCall2 data=ped2.txt vcfFile=test.vcf respectively? If implemented separately, however, how will ParentCall2 detect and utilize half-sibling families from co-parents?
pedigree.txt
CHROM POS ALL ALL ALL ALL ALL ALL ALL ALL ALL
CHROM POS P1_m1 P1_f2 P2_f3 progy_1 progy_2 progy_3 progy_4 progy_5 progy_6
CHROM POS 0 0 0 P1_m1 P1_m1 P1_m1 P1_m1 P1_m1 P1_m1
CHROM POS 0 0 0 P1_f2 P1_f2 P1_f2 P1_f2 P2_f3 P2_f3
CHROM POS 1 2 2 0 0 0 0 0 0
CHROM POS 0 0 0 0 0 0 0 0 0
ped1.txt
CHROM POS P1_m1_P1_f2 P1_m1_P1_f2 P1_m1_P1_f2 P1_m1_P1_f2 P1_m1_P1_f2 P1_m1_P1_f2
CHROM POS P1_m1 P1_f2 progy_1 progy_2 progy_3 progy_4
CHROM POS 0 0 P1_m1 P1_m1 P1_m1 P1_m1
CHROM POS 0 0 P1_f2 P1_f2 P1_f2 P1_f2
CHROM POS 1 2 0 0 0 0
CHROM POS 0 0 0 0 0 0
ped2.txt
CHROM POS P1_m1_P2_f3 P1_m1_P2_f3 P1_m1_P2_f3 P1_m1_P2_f3
CHROM POS P1_m1 P2_f3 progy_5 progy_6
CHROM POS 0 0 P1_m1 P1_m1
CHROM POS 0 0 P2_f3 P2_f3
CHROM POS 1 2 0 0
CHROM POS 0 0 0 0
I also provide the last possible format is on the attachment picture.
Cheers,
chinj cheung
Last edit: chinj cheung 2024-02-25
Dear chinj cheung,
Thank you for your question.
You should include both families in one pedigree. The attached pedigree works for me, and ParentCall2 gives the hint "parent P1_m1 occurs 2 times in the pedigree use halfSibs=1 to utilize this information".
Cheers,
Pasi
Dear Pasi,
Thank you for your response. The ped12.txt file you provided in the attachment seems to be the fourth format mentioned. When executing ParentCall2, should I add the parameter halfSibs=1?
I have another question regarding if both parents of P1_m1 (father), P1_f2, and P2_f3 (two mothers) are known (genotyped or ungenotyped). If I want to provide the parents of both P1_m1 (father), P1_f2, and P2_f3 (two mothers), which would be the progeny's grandfather, should the ped12.txt file be in a similar format as shown in the attachment? Should I also give different family names for each parent of P1_m1?
Best regards,
chinj cheung
Dear Pasi,
Thank you for your response. The ped12.txt file you provided in the attachment seems to be the fourth format mentioned. When executing ParentCall2, should I add the parameter halfSibs=1?
I have another question regarding if both parents of P1_m1 (father), P1_f2, and P2_f3 (two mothers) are known (genotyped or ungenotyped). If I want to provide the parents of both P1_m1 (father), P1_f2, and P2_f3 (two mothers), which would be the progeny's grandfather, should the ped12.txt file be in a similar format as shown in the attachment? Should I also give different family names for each parent of P1_m1?
Best regards,
Dear chinj cheung,
Yes, you should include halfSibs=1 to ParentCall2 if you have shared parents.
You can add the same grandparent in multiple families, just add the different family ID for each column with the same grandparent. Lep-MAP3 does not use the information of same grandparents, it is handled the same way whether the grandparents are unique to a family or not.
Cheers,
Pasi
Dear Pasi,
Thanks for your answers.
yours sincerely
chinj cheung