Hi Pasi,
I got a bug when I use ParentCall2 to convert a vcf file (915765 Sites; 2600MB) to data.call. But there is a problem:
No grandparents present in family F
Number of individuals = 82
Number of families = 1
java.lang.ArrayIndexOutOfBoundsException: 8
at DataParser$VCFParser.parseNext(DataParser.java:511)
at DataParser.getNextLine(DataParser.java:686)
at DataParser.getNextLine(DataParser.java:650)
at ParentCall2.callParents(ParentCall2.java:155)
at ParentCall2.main(ParentCall2.java:1019)
Error 504
Error: Unable to load input file or errors in the file
But when I use only one or two chromsomes VCF file and the same post.txt to do ParentCall2, it is no problem, So it can not be a bug of post.txt.
part of the post.txt:
CHR POS F F F F F F F F F F F F F F F F F
CHR POS LM50-2 3-85-1 1_1 1_10 1_11 1_12 1_13 1_14 1_15 1_16 1_17 1_18 1_19 1_2 1_20 1_21 1_22
CHR POS 0 0 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2
CHR POS 0 0 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1
CHR POS 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CHR POS 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Could you help me to solve this problem?
Thank you,
Felix
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thank you Pasi, I have solved this problem,
Problem is that, the outfile of bcftools 'concat' will cause this bug, but the commond of vcftools concat will report no error.
Wish this can help others.
Best wish,
Felix
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Pasi,
I got a bug when I use ParentCall2 to convert a vcf file (915765 Sites; 2600MB) to data.call. But there is a problem:
No grandparents present in family F
Number of individuals = 82
Number of families = 1
java.lang.ArrayIndexOutOfBoundsException: 8
at DataParser$VCFParser.parseNext(DataParser.java:511)
at DataParser.getNextLine(DataParser.java:686)
at DataParser.getNextLine(DataParser.java:650)
at ParentCall2.callParents(ParentCall2.java:155)
at ParentCall2.main(ParentCall2.java:1019)
Error 504
Error: Unable to load input file or errors in the file
But when I use only one or two chromsomes VCF file and the same post.txt to do ParentCall2, it is no problem, So it can not be a bug of post.txt.
part of the post.txt:
CHR POS F F F F F F F F F F F F F F F F F
CHR POS LM50-2 3-85-1 1_1 1_10 1_11 1_12 1_13 1_14 1_15 1_16 1_17 1_18 1_19 1_2 1_20 1_21 1_22
CHR POS 0 0 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2 LM50-2
CHR POS 0 0 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1 3-85-1
CHR POS 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
CHR POS 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Could you help me to solve this problem?
Thank you,
Felix
Thank you Pasi, I have solved this problem,
Problem is that, the outfile of bcftools 'concat' will cause this bug, but the commond of vcftools concat will report no error.
Wish this can help others.
Best wish,
Felix