Genetic map from scrna-seq

[Ana Kurdadze]

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)
    at java.base/java.lang.Integer.parseInt(Integer.java:662)
    at DataParser.getNextLine(DataParser.java:750)
    at DataParser.getNextLine(DataParser.java:662)
    at ParentCall2.callParents(ParentCall2.java:118)
    at ParentCall2.main(ParentCall2.java:1225)
Error 504
Error: Unable to load input file or errors in the file

Thanks ahead!

[Pasi Rastas]

Dear Ana,

Thank you for your question.

Please search the discussions with word "haploid", it seemed to find many relevant topics that might help you (sorry for my lazy answer). Lep-MAP3 can analyse you data, but you have to "trick" Lep-MAP3 to think the data is in one of its supported formats F1/F2/selfing cross.

Anyway, I checked you pedigree and you should add two parents to your family (real parent and dummy, or grandparent(s) and dummy parents). Now the other parent is 0 that does not pass Lep-MAP3. Also note that pedigree should be transposed, I created the proper pedigree with the command:

transpose_tab pedigree.ped|awk '{print "CHR\tPOS\t"$0}' >ped_t.txt

Cheers,
Pasi

Ps. please include the commands you have run (e.g. java ParentCall data=ped_t), it is difficult to know the problem from the mere error messages.

[Ana Kurdadze]

Hi Pasi,

Thanks a lot for the quick response!

After reading some discussions, I tried the following:

1. Add PATERNAL_PAT as grandparent, variant sites 1/1
2. Add DUMMY_MAT as dummy_gp, always 0/0
3. Add DUMMY_F1_PAT as offspring, 0/1 at every site where PATERNAL_PAT is 1/1
4. 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 of grandparents (4 and 2) in family Fam1
Found 2 grandparents in family Fam1
Number of individuals = 26216
Number of families = 1
Error 517
Error: Individual names not found from the vcf file

I’ve attached a small subset of the VCF and the transformed pedigree. I’d greatly appreciate it if you could take a look.

Thanks a lot!

[Ana Kurdadze]

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 !