Ana Kurdadze

Hi Pasi, In my .vcf file I have 13300 male gametes (after filtering) and more than 24000 variant sites genotyped. Yet even with changing around parameters, I only manage to get up to 800 markers, few of them fall into LGs and they can not be reliably ordered within the groups. The data is very sparse, on aveage 95% of markers are missing from every cell. Do you have any suggestion how to mitigate the sparsity of the data? Please let me know if you need more information or test data. Thanks, Ana

Hi Pasi, In my .vcf file I have 13300 male gametes sequenced and more than 24000 variant sites genotyped. Yet even with changing around parameters, I only manage to get up to 800 markers, few of them fall into LGs and they can not be reliably ordered within the groups. The data is very sparse, on aveage 95% of markers are missing from every cell. Do you have any suggestion how to mitigate the sparsity of the data? Please let me know if you need more information or test data. Thanks, Ana

Hi Pasi, I found this solution in the discussions, and it appears to resolve the issue. zcat $PAT_CELL_VCF|$JAVA -cp $BIN ParentCall2 \ data=$PEDIGREE \ vcfFile=- \ removeNonInformative=1 > $OUT_DATA Thanks !

Hi Pasi, Thanks a lot for the quick response! After reading some discussions, I tried the following: Add PATERNAL_PAT as grandparent, variant sites 1/1 Add DUMMY_MAT as dummy_gp, always 0/0 Add DUMMY_F1_PAT as offspring, 0/1 at every site where PATERNAL_PAT is 1/1 Add DUMMY_F1_MAT always 0/0 This the command I run: $JAVA -cp $BIN ParentCall2 \ data=$PEDIGREE \ vcfFile=$PAT_CELL_VCF \ removeNonInformative=1 > $OUT_DATA After multiple attempts, I still get the following error Warning: Different number...

Hi Pasi, Thanks a lot for the quick response! After reading some discussions, I tried the following: Add PATERNAL_PAT as grandparent, variant sites 1/1 Add DUMMY_MAT as dummy_gp, always 0/0 Add DUMMY_F1_PAT as offspring, 0/1 at every site where PATERNAL_PAT is 1/1 Add DUMMY_F1_MAT always 0/0 This the command I run: $JAVA -cp $BIN ParentCall2 \ data=$PEDIGREE \ vcfFile=$PAT_CELL_VCF \ removeNonInformative=1 > $OUT_DATA ``` I still get the following error Warning: Different number of grandparents (4...

Hi Pasi, Thanks a lot for the software! I have scRna-seq data from over 26000 pollen cells from F1 sample. I also have variant sites from alignment of the paternal reads to the maternal reference genome. I am running ParentCall2 in halfSibs=1 mode. I have attached the pedigree. I'm getting error java.lang.NumberFormatException: For input string: "PARENT_PAT" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) at java.base/java.lang.Integer.parseInt(Integer.java:565)...

Hi Pasti, Thanks a lot for the software! I have scRna-seq data from over 26000 pollen cells from F1 sample. I also have variant sites from alignment of the paternal reads to the maternal reference genome. I am running ParentCall2 in halfSibs=1 mode. I have attached the pedigree. I'm getting error java.lang.NumberFormatException: For input string: "PARENT_PAT" at java.base/java.lang.NumberFormatException.forInputString(NumberFormatException.java:67) at java.base/java.lang.Integer.parseInt(Integer.java:565)...