Activity for chinj cheung
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chinj cheung posted a comment on discussion General Discussion
Dear pasi, Thank you for your reply. thanks, Chinj Cheung
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Dear pasi, Yes! I have approximately 1200 single-parent families and around 200 two-parent families. To clarify, when running ParentCall2, should I add the parameters familyLimit=1(1.5) and ignoreParentOrder=1, where ignoreParentOrder means that the order of the parents' genotypes need not be taken into account? But this statement "makes the map construction more difficult (it requires extra parameters in other modules as well)" implies that I should pay attention to what during the subsequent map...
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Dear pasi, The VCF file contains 6715 samples, with over 4000 individuals whose sample IDs can be found in pedigree.txt. There are more than 1000 families, each of which includes parents who have at least one genotype and their offsprings also have genotypes. I am unsure if it is problematic for only the father or mother to be genotyped in the parents' case. In the screenshot I provided above, the familyID is LL14CLA17701435_LL22RK917700771. Among them, LL22RK917700771 has a genotype in the vcf file,...
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The VCF file contains 6715 samples, with over 4000 individuals whose sample IDs can be found in pedigree.txt. There are more than 1000 families, each of which includes parents who have at least one genotype and their offsprings also have genotypes. I am unsure if it is problematic for only the father or mother to be genotyped in the parents' case. In the screenshot I provided above, the familyID is LL14CLA17701435_LL22RK917700771. Among them, LL22RK917700771 has a genotype in the vcf file, while...
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The VCF file contains 6715 samples, with over 4000 individuals whose sample IDs can be found in pedigree.txt. There are more than 1000 families, each of which includes parents who have at least one genotype and their offsprings also have genotypes. I am unsure if it is problematic for only the father or mother to be genotyped in the parents' case.
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When lod=1, the values of theta are 0.08, 0.02, and 0.04. At this time, there are still only two LGs.
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Hi Pasi! I used ParentCall2 to convert a .vcf.gz file to data.call.gz, but I noticed that most of the values in data.call.gz are 1. I'm not sure what the problem is. The .vcf file was generated from chip genotypes using plink, so it only contains FMT/GT information and does not include likelihood values. The most important thing is that I only got two LGs by SeparateChromosomes2（lod=10 theta=0.08）; but my family has 1483； Thanks, chinj cheung
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Dear Pasi, Thanks for your answers. yours sincerely chinj cheung
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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...
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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...
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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...
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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...
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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_1,...; 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...
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